diff --git a/Pipfile b/Pipfile index 44984a1..9a780f0 100644 --- a/Pipfile +++ b/Pipfile @@ -39,6 +39,9 @@ jupyterlab = "*" pandas = "*" pandas-stubs = "*" matplotlib = "*" +scikit-learn = "*" +scipy = "*" +seaborn = "*" [requires] python_version = "3.12" diff --git a/Pipfile.lock b/Pipfile.lock index 4bef2fb..cc84b46 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "b34ab7cdaff0e13bf4227b9658bd5393a414b527b4bc3926305ff4fd91ed043f" + "sha256": "d353fd9554699eba1a844b55711c58acf4e30f28e4a787952c7396f953652fe4" }, "pipfile-spec": 6, "requires": { @@ -656,12 +656,12 @@ }, "setuptools": { "hashes": [ - "sha256:b8b8060bb426838fbe942479c90296ce976249451118ef566a5a0b7d8b78fb05", - "sha256:bd63e505105011b25c3c11f753f7e3b8465ea739efddaccef8f0efac2137bac1" + "sha256:f171bab1dfbc86b132997f26a119f6056a57950d058587841a0082e8830f9dc5", + "sha256:fe384da74336c398e0d956d1cae0669bc02eed936cdb1d49b57de1990dc11ffc" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==70.2.0" + "version": "==70.3.0" }, "shellingham": { "hashes": [ @@ -1605,11 +1605,11 @@ }, "genebe": { "hashes": [ - "sha256:1b58b303ae3a28718c24d33d1164a7e214bb5b853906331ba8236c0d299b6258", - "sha256:5bf429adbe0af32b70941b49ae26742b3b3e258da61b679a7033424bdc968f93" + "sha256:b96a77091c77a98d90ede87beb3cdc3bccc3f215b9f519a72d86ee25b83e171a", + "sha256:fdaf0c70e7201a33453c97b5f75d6cec8bde016e8742d55a98140843e1466f00" ], "index": "pypi", - "version": "==0.0.18" + "version": "==0.1.1" }, "genson": { "hashes": [ @@ -1730,6 +1730,14 @@ "markers": "python_version >= '3.7'", "version": "==3.1.4" }, + "joblib": { + "hashes": [ + "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6", + "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e" + ], + "markers": "python_version >= '3.8'", + "version": "==1.4.2" + }, "json5": { "hashes": [ "sha256:34ed7d834b1341a86987ed52f3f76cd8ee184394906b6e22a1e0deb9ab294e8f", @@ 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"sha256:636f8336facf092165e27924f223d3c62ca560b1f2bb5dff7ab7fad265361987", + "sha256:93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7" + ], + "index": "pypi", + "markers": "python_version >= '3.8'", + "version": "==0.13.2" + }, "send2trash": { "hashes": [ "sha256:0c31227e0bd08961c7665474a3d1ef7193929fedda4233843689baa056be46c9", @@ -3171,12 +3248,12 @@ }, "setuptools": { "hashes": [ - "sha256:b8b8060bb426838fbe942479c90296ce976249451118ef566a5a0b7d8b78fb05", - "sha256:bd63e505105011b25c3c11f753f7e3b8465ea739efddaccef8f0efac2137bac1" + "sha256:f171bab1dfbc86b132997f26a119f6056a57950d058587841a0082e8830f9dc5", + "sha256:fe384da74336c398e0d956d1cae0669bc02eed936cdb1d49b57de1990dc11ffc" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==70.2.0" + "version": "==70.3.0" }, "six": { "hashes": [ @@ -3299,6 +3376,14 @@ "markers": "python_version >= '3.8'", "version": "==0.18.1" }, + "threadpoolctl": { + "hashes": [ + "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107", + "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467" + ], + "markers": "python_version >= '3.8'", + "version": "==3.5.0" + }, "tinycss2": { "hashes": [ "sha256:152f9acabd296a8375fbca5b84c961ff95971fcfc32e79550c8df8e29118c54d", diff --git a/src/bench/cohens_kappa_results.csv b/src/bench/cohens_kappa_results.csv new file mode 100644 index 0000000..5fb4767 --- /dev/null +++ b/src/bench/cohens_kappa_results.csv @@ -0,0 +1,16 @@ +Criteria,AutoACMG Kappa,Intervar Kappa,Genebe Kappa +PVS1,0.9059419881723458,0.23490212411495204,0.9529709940861729 +PS1,0.34816549570647926,0.0,0.7080419580419581 +PM1,-0.005815160955348064,0.32813678652250433,0.6100233518950962 +PM2,-0.3840759368137707,0.5030122668215142,0.5405444540978859 +PM4,1.0,0.0,0.660569105691057 +PM5,0.6311549954527738,0.10098385000928167,0.6754315765405281 +PP2,0.0,-0.06556655665566558,0.8062817881681092 +PP3,0.28326180257510725,0.5914587264975187,0.7549882629107981 +BA1,0.0,0.10098385000928167,0.7562636828022379 +BS1,-0.011178388448998433,-0.06099110546378639,0.5831253120319521 +BS2,-0.011588095865156633,0.10199479618386809,0.49288796547866387 +BP1,0.0,0.34232050893668586,0.9267543859649123 +BP3,0.7970838396111786,0.0,0.0 +BP4,-0.20113023375288974,0.6171480972031178,0.9327245870820464 +BP7,0.7277469840234757,0.7874158937988726,0.9129150008691118 diff --git a/src/bench/comparison_criteria_custom.csv b/src/bench/comparison_criteria_custom.csv index 1d0c297..07148d1 100644 --- a/src/bench/comparison_criteria_custom.csv +++ b/src/bench/comparison_criteria_custom.csv @@ -176,5 +176,7 @@ NM_001754.4(RUNX1):c.952T>G,BA1;BP4,"This missense variant is present in gnomAD NM_001754.4(RUNX1):c.183G>A,BA1;BP2;BP4,"This synonymous variant is present in gnomAD (v2 and v3) at an allele frequency >0.15% with at least >5 alleles in any general continental population (BA1); in addition, the variant was found in homozygosity in the population database (BP2). Although evolutionary conservation prediction algorithms predict the site as being moderately conserved (PhyloP score: 3.03 > 0.1 [-14.1;6.4]) and the variant is not the reference nucleotide in one primate and/or three mammal species, it is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created (BP4). In summary, the clinical significance of this variant is benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, and BP4." NM_001754.4(RUNX1):c.144C>T,BA1;BP2;BP4;BP7,"This synonymous variant is present in gnomAD (v2 and v3) at an allele frequency >0.15% with at least 5 alleles in any general continental population (BA1); in addition, the variant was found in homozygosity in the population database (BP2). The variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created, and evolutionary conservation prediction algorithms predict the site as being not highly conserved (PhyloP score: 1.01 [-14.1;6.4]) (BP4; BP7). In summary, the clinical significance of this variant is benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4 and BP7." NM_000212.2(ITGB3):c.342T>C,BA1;BP4;BP7,"The NM_000212.2:c.342T>C variant, which leads to a synonymous change, Ile114Ile, is reported at a high frequency in the African population in gnomAD and ExAC (0.05). In-silico splicing predictors do not predict splicing impact. PMID: 27469266 reports on this and other polymorphic, non-causal variants found in linkage disequilibrium with deleterious mutations in GT patients. Ile114Ile is classified as a benign variant. GT-specific criteria applied: BA1, BP4, and BP7." - - +#BP3,, +NM_005249.4(FOXG1):c.209_232del24,BA1;BS2;BP3;BP5,"The allele frequency of the p.Q70_P77del variant in FOXG1 is 0.03% in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The p.Q70_P77del variant is observed in at least 2 unaffected individuals (internal database) (BS2). The p.Q70_P77del variant is an in-frame deletion present in a repetitive region of FOXG1 (BP3). The p.Q70_P77del variant is found in at least 3 patients with an alternate molecular basis of disease (internal database) (BP5_strong). In summary, the p.Q70_P77del variant in FOXG1 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP3, BP5_strong)." +NM_005249.5(FOXG1):c.209_235del,BA1;BS2;BP3,"The allele frequency of the c.209_235del variant in FOXG1 is 0.17% in Ashkenazi Jewish sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions BA1). The p.Gln70_Pro78del variant is observed in at least 2 unaffected individuals (GeneDx internal database) (BS2). The p.Gln70_Pro78del variant is an in-frame deletion present in a repetitive region of FOXG1 (BP3). In summary, the p.Gln70_Pro78del variant in FOXG1 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP3)." +NM_005249.5(FOXG1):c.237_239del,BA1;BP3,"The highest population minor allele frequency of the c.237_239del (p.Pro80del) variant in FOXG1 in gnomAD v4.1 is 0.00054 in the East Asian population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1). The p.Pro80del variant is an in-frame deletion present in a repetitive region of FOXG1 (BP3). In summary, the p.Pro80del variant in FOXG1 is classified as a benign variant based on the ACMG/AMP criteria (BA1, BP3)." diff --git a/src/bench/comparison_v3.py b/src/bench/comparison_v3.py index 3107b5d..eca01e6 100644 --- a/src/bench/comparison_v3.py +++ b/src/bench/comparison_v3.py @@ -100,9 +100,10 @@ def intervar_response(variant: str): url = ( f"http://wintervar.wglab.org/api_new.php?" - f"queryType=position&chr={chromosome}&pos={position}" + f"queryType={position}&chr={chromosome}&pos={position}" f"&ref={reference}&alt={alternative}&build=hg19" ) + print("Requesting:", url) backend_resp = requests.get(url) backend_resp.raise_for_status() return backend_resp.json() @@ -132,6 +133,7 @@ def genebe_response(variant: str): f"chr={chromosome}&pos={position}" f"&ref={reference}&alt={alternative}&genome=hg38" ) + print("Requesting:", url) backend_resp = requests.get(url) backend_resp.raise_for_status() return backend_resp.json() @@ -237,7 +239,7 @@ def eval_genebe(resp, expected): ] ) -for i, var in enumerate(variants): +for i, var in enumerate(variants[-3:]): # Save the stats every 10 variants if i % 50 == 0: print(f"Processed {i} variants") diff --git a/src/bench/correlation_matrix.csv b/src/bench/correlation_matrix.csv new file mode 100644 index 0000000..4f34766 --- /dev/null +++ b/src/bench/correlation_matrix.csv @@ -0,0 +1,5 @@ +,AutoACMG,Intervar,Genebe,ClinGen +AutoACMG,1.0,0.008763199951854865,0.28831332823829237,0.11973512248675762 +Intervar,0.008763199951854816,1.0,0.6729186674369368,0.7965249163017614 +Genebe,0.28831332823829237,0.6729186674369367,1.0,0.8001863441995085 +ClinGen,0.11973512248675768,0.7965249163017614,0.8001863441995085,1.0 diff --git a/src/bench/results.csv b/src/bench/results.csv index 6242803..163df77 100644 --- a/src/bench/results.csv +++ b/src/bench/results.csv @@ -1,165 +1,168 @@ -Variant,Expected Criteria,AutoACMG Criteria,AutoACMG Prediction time,AutoACMG True Positives,AutoACMG False Negatives,AutoACMG False Positives,Intervar Criteria,Intervar Prediction time,Intervar True Positives,Intervar False Negatives,Intervar False Positives,Genebe Criteria,Genebe Prediction time,Genebe True Positives,Genebe False Positives,Genebe False Negatives,Comment -4-113568536-G-GA,PVS1,PVS1;PM1;PM2,3.32929086685181,PVS1,PM1;PM2,,,0,,,,,0.268923759460449,,,PVS1,Gene: LARP7 -NM_004360.3:c.1085delT,PVS1,PVS1;PM1,1.59775352478027,PVS1,PM1,,,0,,,,PVS1;PS4;PM2;PM5,0.307955503463745,PVS1,PS4;PM5;PM2,,Gene: CDH1; p.Val362GlyfsTer31; From Recommendation 07.09.2018 -NM_000152.4:c.525delT,PVS1,PVS1;PM1;PM2,1.64967465400696,PVS1,PM1;PM2,,,0,,,,PVS1;PM2;PM3;PP4,0.361843109130859,PVS1,PM3;PP4;PM2,,Gene: GAA; p.Glu176ArgfsTer45; From Recommendation 07.09.2018 -NM_000152.4:c.1987delC,PVS1,PVS1;PM1,1.53102111816406,PVS1,PM1,,,0,,,,PVS1;PM2;PP5,0.339899063110351,PVS1,PP5;PM2,,Gene: GAA; p.Gln663SerfsTer33; From Recommendation 07.09.2018 -NM_000152.4:c.2706delG,PVS1,PVS1;PM1,1.39712834358215,PVS1,PM1,,,0,,,,PVS1;PM2;PM3;PP4,0.344012498855591,PVS1,PM3;PP4;PM2,,Gene: GAA; p.Lys903ArgfsTer2; From Recommendation 07.09.2018 -NM_000218.2:c.567dupG,PVS1,PVS1;PM1,1.47669363021851,PVS1,PM1,,,0,,,,PVS1;PM2;PP5,0.334547519683838,PVS1,PP5;PM2,,Gene: KCNQ1; p.Arg190AlafsTer14; From Recommendation 07.09.2018 -NM_000218.2:c.1343dupC,PVS1,PVS1;PM1;PM2,1.5736825466156,PVS1,PM1;PM2,,,0,,,,PVS1;PP5,0.353738069534302,PVS1,PP5,,Gene: KCNQ1; p.Glu449ArgfsTer14; From Recommendation 07.09.2018 -NM_000441.1:c.365dupT,PVS1,PVS1;PM1;PM2,1.56346273422241,PVS1,PM1;PM2,,,0,,,,PVS1;PM2;PM3;PP4,0.35863447189331,PVS1,PM3;PP4;PM2,,Gene: SLC26A4; p.Pro123SerfsTer4; From Recommendation 07.09.2018 -NM_206933.2:c.4338_4339delCT,PVS1,PVS1;PM1;PM2,1.48185229301453,PVS1,PM1;PM2,,,0,,,,PVS1;PM2;PM3;PP1;PP4,0.375017404556274,PVS1,PM3;PP1;PP4;PM2,,Gene: USH2A; p.Cys1447GlnfsTer29; From Recommendation 07.09.2018 -NM_206933.2:c.4510dupA,PVS1,PVS1,1.41564512252808,PVS1,,,,0,,,,PVS1;PM2;PM3;PP4,0.32335090637207,PVS1,PM3;PP4;PM2,,Gene: USH2A; p.Arg1504LysfsTer26; From Recommendation 07.09.2018 -NM_004004.5:c.235delC,PVS1,PVS1;PM1;PM2,1.57983469963074,PVS1,PM1;PM2,,,0,,,,PVS1;PS3;PM3;BS1,0.33725094795227,PVS1,PM3;PS3;BS1,,Gene: GJB2; p.Leu79CysfsTer3; From Recommendation 07.09.2018 -NM_004004.5:c.35delG,PVS1,PVS1;PM1;PM2,1.52198648452759,PVS1,PM1;PM2,,,0,,,,PVS1;PS4;PM3;BA1,0.296200752258301,PVS1,PM3;PS4;BA1,,Gene: GJB2; p.Gly12ValfsTer2; From Recommendation 07.09.2018 -NM_004004.5:c.167delT,PVS1,PVS1;PM1;PM2,1.42025852203369,PVS1,PM1;PM2,,,0,,,,PVS1;PM3;BA1,0.350803375244141,PVS1,PM3;BA1,,Gene: GJB2; p.Leu56ArgfsTer26; From Recommendation 07.09.2018 -NM_000277.1:c.822_832del,PVS1,PVS1;PM1,1.40451002120972,PVS1,PM1,,,0,,,,PVS1;PM2;PM3;PP4,0.305345773696899,PVS1,PM3;PP4;PM2,,Gene: PAH; p.Lys274AsnfsTer5; From Recommendation 07.09.2018 -NM_000277.2:c.632delC,PVS1,PVS1;PM1;PM2,1.58016014099121,PVS1,PM1;PM2,,,0,,,,PVS1;PM2;PM3;PP4,0.294129848480225,PVS1,PM3;PP4;PM2,,Gene: PAH; p.Pro211HisfsTer130; From Recommendation 07.09.2018 -NM_000314.6:c.50_51delAA,PVS1,PVS1;PM1,1.42956137657166,PVS1,PM1,,,0,,,,PVS1;PS4;PM2,0.290371179580688,PVS1,PS4;PM2,,PTEN -NM_000277.2:c.47_48del,PVS1,PVS1;PM1,1.36341953277588,PVS1,PM1,,,0,,,,PVS1;PM2;PM3;PP4,0.317233800888062,PVS1,PM3;PP4;PM2,,Gene: PAH; p.Ser16Ter; From Recommendation 07.09.2018 -NM_000277.2:c.1147C>T,PVS1,PVS1;PM1,1.71908473968506,PVS1,PM1,,PVS1;PM2;PP3;PP5,0.364331007003784,PVS1,,PP3;PP5;PM2,PVS1;PM2;PM3;PP4,0.312084913253784,PVS1,PM3;PP4;PM2,,Gene: PAH; p.Gln383Ter; From Recommendation 07.09.2018 -NM_004360.3:c.1792C>T,PVS1,PVS1;PM1,1.67226600646973,PVS1,PM1,,PVS1;PM2;PP3;PP5,0.398955106735229,PVS1,,PP3;PP5;PM2,PVS1;PS2;PS4;PM2;PM5;PP1,0.355690956115723,PVS1,PM5;PP1;PM2;PS2;PS4,,Gene: CDH1; p.Arg598Ter; From Recommendation 07.09.2018 -NM_000314.6:c.1003C>T,PVS1,PVS1;PM1,1.74338698387146,PVS1,PM1,,PVS1;PM2;PP3;PP5,0.430862426757813,PVS1,,PP3;PP5;PM2,PVS1;PM2;PP5,0.325910568237305,PVS1,PP5;PM2,,PTEN -NM_000152.4:c.1A>G,PVS1,PVS1;PM1,1.74510979652405,PVS1,PM1,,PM2;PP5,0.356374740600586,,PVS1,PP5;PM2,PVS1;PS1;PM2;PP5,0.310552835464477,PVS1,PS1;PP5;PM2,,Gene: GAA; p.Met1Val; From Recommendation 07.09.2018 -NM_000218.2:c.2T>C,PVS1,PM1,1.71596670150757,,PM1,PVS1,PM2;PP3,0.358755111694336,,PVS1,PP3;PM2,PVS1;PM2,0.302855968475342,PVS1,PM2,,Gene: KCNQ1; p.Met1Thr; From Recommendation 07.09.2018 -NM_000277.2:c.1A>G,PVS1,PM1;PP3;BP4,1.64721179008484,,PM1;BP4;PP3,PVS1,PS3;PM2;PP3;PP5,0.359246492385864,,PVS1,PP3;PP5;PS3;PM2,PS3;PM2;PM3;PP4,0.303873777389526,,PM3;PS3;PP4;PM2,PVS1,Gene: PAH; p.Met1Val; From Recommendation 07.09.2018 -NM_000314.6:c.3G>T,PVS1,PM1,1.72468209266663,,PM1,PVS1,PM2;PP3,0.361842393875122,,PVS1,PP3;PM2,PVS1;PS1;PM2,0.291746616363525,PVS1,PS1;PM2,,Gene: PTEN; p.Met1Ile; From Recommendation 07.09.2018 -NM_176795.4(HRAS):c.173C>T,PS1;PS4;PM1;PM2;PM6;PP2;PP3,PM1;PP3;BP4,189.004821538925,PP3;PM1;PM2,BP4,PP2;PS1,PM1;PM2;PP3;PP5,0.4151291847229,PP3;PM2;PM1,PS1;PS4;PP2;PM6,PP5,PM1;PM2;PP3;PP5,0.320986270904541,PP3;PM1;PM2,PP5,PP2;PM6;PS4;PS1,from ClinGen https://erepo.clinicalgenome.org/evrepo/ui/classification/4fa14d9d-3bce-4dd8-affa-771b6298c4fc -NM_000277.2(PAH):c.503delA,PVS1;PM2;PP4,PVS1;PM1;PM2,1.39300084114075,PM2;PVS1,PM1,PP4,,0,,,,PVS1;PM2;PP4,0.311551809310913,PVS1;PP4;PM2,,,"PAH-specific ACMG/AMP criteria applied: PVS1: Frameshift variant; PM2: Extremely low frequency. ExAC MAF: 0.00001.; PP4: Detected in PKU patient in international phase II clinical trial for sapropterin. (PMID:23430918). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PVS1, PM2, PP4)." -NM_000277.1(PAH):c.814G>T,PVS1;PM2;PP4,PVS1;PM1;PM2,1.78998494148254,PM2;PVS1,PM1,PP4,PVS1;PM2;PP3;PP5,0.366233825683594,PVS1;PM2,PP4,PP3;PP5,PVS1;PM2;PP4,0.341337919235229,PVS1;PP4;PM2,,,"PAH-specific ACMG/AMP criteria applied: PM2: Absent from 1000G, ESP. Extrememly low frequency in ExAC, gnomAD (MAF= 0.00006, 0.0003093); PVS1: Nonsense variant. Predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay.; PP4: G272X found on one allele of a patient with classic PKU (PMID:1975559). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PVS1, PP4)." -NM_000277.1(PAH):c.1162G>A,PS3;PM2;PM3;PP3;PP4,PM1;PM2;PM5;PP3;BP4,7.61773657798767,PM2;PP3,PM1;PM5;BP4,PS3,PM1;PM2;PP3;PP5;BP1,0.374915599822998,PP3;PM2,PP4;PS3;PM3,PP5;BP1;PM1,PS3;PM2;PM3;PP3;PP4,0.311354875564575,PM3;PP3;PS3;PM2;PP4,,,"PAH-specific ACMG/AMP criteria applied: PM2: Extremely low in ExAC and 1000 genomes (PMID:9860305); PS3: PAH activity in COS cell expression system 15% (PMID:9860305); PM3: Compound het with severe mutation (PMID:9860305); PP3: ; PP4: Reported in patient with classic PKU (PMID:9860305). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PS3, PM3, PP3, PP4)." -NM_000257.3(MYH7):c.3036C>T,BA1;BP7,PM2;BP7,2.65372490882874,BP7,PM2,BA1,PM2;BP4;BP6;BP7,0.369901895523071,BP7,BA1,BP6;BP4;PM2,BA1;BP7,0.317893028259277,BP7;BA1,,,"The filtering allele frequency of the c.3036C>T (p.Ala1012=) silent variant in the MYH7 gene is 0.7% (137/16512) of South Asian chromosomes by the Exome Aggregation Consortium (http://exac.broadinstitute.org), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Inherited Cardiomyopathy Expert Panel (BA1, BP7; PMID:29300372)." -NM_000156.6(GAMT):c.279C>T,BA1;BP4;BP7,PM2;BP7,2.99034929275513,BP7;BP4,PM2,BA1,BP4;BP6;BP7,0.342584133148193,BP7;BP4,BA1,BP6,BA1;BP4;BP7,0.314168930053711,BP4;BP7;BA1,,,"The NM_000156.6:c.279C>T (p.Asp93=) is a synonymous variant in GAMT that is predicted to not impact splicing by SpliceAI and VarSeak, and the nucleotide is not highly conserved (BP4, BP7). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00484 (87/17976 alleles) in the East Asian population, which is higher than the ClinGen CCDS VCEP’s threshold for BA1 (>0.003), and therefore meets this criterion (BA1). This variant does not appear to have been previously reported in the published literature. It is noted in ClinVar (Variation ID 137434). In summary, this variant meets the criteria to be classified as benign for GAMT deficiency. GAMT-specific ACMG/AMP codes met, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): BA1, BP4, BP7.(Classification approved by the ClinGen CCDS VCEP on June 6, 2022)." -NM_004700.3(KCNQ4):c.720C>G,BP4;BP7,PM1;BP7,2.16768383979797,BP7,PM1,BP4,PM2;BP4;BP6;BP7,0.383844614028931,BP7;BP4,,BP6;PM2,BP4;BP7,0.323836803436279,BP4;BP7,,,"The silent p.Thr240= variant in KCNQ4 is not predicted by computational tools to impact splicing (BP7. BP4). The variant is absent from the Genome Aggregation Database (http://gnomad.broadinstitute.org), however this is not considered evidence against a likely benign classification. In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied: BP7, BP4." -NM_004985.4(KRAS):c.451-14T>C,BP4;BP7,PM1;PM2;BP7,2.11770963668823,BP7,PM1;PM2,BP4,,0,,,,BP4;BP7,0.302630424499512,BP4;BP7,,,"The c.451-14T>C variant in KRAS has been seen in 3 cases undergoing RASopathy panel testing (PS4 not met; LMM, GeneDx internal data; GTR ID: 26957, 21766; ClinVar SCV000170023.9, SCV000198459.4) is an intronic variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Computational prediction tools and conservation analysis suggest that the variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as likely benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BP4, BP7." -NM_005343.3(HRAS):c.510G>A,BP4;BP5;BP7,PM2;BP7,1.92048192024231,BP7,PM2,BP4,PM2;BP4;BP6;BP7,0.363871812820435,BP7;BP4,BP5,BP6;PM2,BS1;BS2;BP4;BP6;BP7,0.339710474014282,BP4;BP7,BS1;BS2;BP6,BP5,"The c.510G>A (p.Lys170=) variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Computational prediction tools and conservation analysis suggest that the p.Lys170= variant does not impact the protein (BP4).This variant has been identified in a patient with an alternate molecular basis for disease (BP5; LMM and GeneDx internal data; GTR ID's: 21766, 26957; ClinVar SCV000062144; SCV000168832). In summary, this variant meets criteria to be classified as likely benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BP7, BP5, BP4." -NM_004333.4(BRAF):c.111G>A,BP5;BP7,PM2;BP7,2.05794048309326,BP7,PM2,BP5,PM2;BP4;BP6;BP7,1.38652539253235,BP7,BP5,BP6;BP4;PM2,BP5;BP7,0.299437761306763,BP5;BP7,,,"The c.111G>A (p.Ser37=) variant in BRAF is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). This variant has been identified in a patient with an alternate molecular basis for disease (BP5; Partners LMM, GeneDx internal data, GTR ID's: SCV000197179.4, SCV000512270.5). In summary, this variant meets criteria to be classified as likely benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BP7, BP5." -NM_000152.5(GAA):c.1332T>C,BS1;BP4;BP7,PM1;PM2;BP7,1.9147162437439,BP7;BS1,PM1;PM2,BP4,PM2;BP4;BP6;BP7,0.384311676025391,BP7;BP4,BS1,BP6;PM2,BS1;BP4;BP7,0.324812889099121,BS1;BP4;BP7,,,"The NM_000152.5:c.1332T>C (p.Pro444=) variant in GAA is a synonymous (silent) variant that is not predicted to impact splicing; the nucleotide is not highly conserved (PhyloP 100 way score is -2.4 (BP4, BP7). There is a ClinVar entry for this variant (Variation ID: 286018). In summary, this variant meets the criteria to be classified as likely benign for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases VCEP (Specifications Version 2.0): BS1, BP4, BP7.(Classification approved by the ClinGen Lysosomal Diseases VCEP, March 13, 2023)." -NM_001754.4(RUNX1):c.1317C>T,PM2;BP4;BP7,BP7,1.76365494728088,PM2;BP7,,BP4,PM2;BP4;BP6;BP7,0.358675479888916,BP7;BP4;PM2,,BP6,PM2;BP4;BP7,0.354830503463745,BP4;BP7;PM2,,,"Although this variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2), the synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score: -0.44 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7, PM2." -NM_001754.4(RUNX1):c.36G>A,BP4;BP7,PM2;BP7,1.98864221572876,BP7,PM2,BP4,BP4;BP6;BP7,0.367478609085083,BP7;BP4,,BP6,BP4;BP7,0.310839653015137,BP4;BP7,,,"This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created. In addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score: -1.41 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7." -NM_001754.4(RUNX1):c.843C>T,BP4;BP7,PM1;BP7,1.88208746910095,BP7,PM1,BP4,BP4;BP6;BP7,1.40275645256042,BP7;BP4,,BP6,BP4;BP7,0.325880765914917,BP4;BP7,,,"This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -2.38 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7." -NM_005633.3(SOS1):c.1230G>A,BA1;BP4;BP5;BP7,PM2;BP7,1.99886441230774,BA1;BP7;BP4,PM2,BP5,BP4;BP6;BP7;BS1;BS2,0.367127656936645,BP7;BP4,BP5;BA1,BP6;BS1;BS2,BA1;BP4;BP5;BP7,0.294578552246094,BP4;BP5;BP7;BA1,,,"The c.1230G>A (p.Gln410=) variant in SOS1 has been identified in a patient with an alternate molecular basis for disease (BP5; Partners LMM internal data GTR Lab ID: 21766 ClinVar SCV000062189.5). This variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Computational prediction tools and conservation analysis suggest that the p.Gln410= variant does not impact the protein (BP4). The filtering allele frequency of the c.1230G>A (p.Gln410=) variant in the SOS1 gene is 4.69% for Latino chromosomes by the Exome Aggregation Consortium (580/11526 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP5, BP7, BP4." -NM_004700.3(KCNQ4):c.825G>C,PM1;PM2;PM5;PP3,PM1;PP3;BP4,7.50642442703247,PM1;PM5;PP3,BP4,PM2,PM1;PM2;PP3;PP5,0.399600028991699,PP3;PM2;PM1,PM5,PP5,PM1;PM2;PM5;PP3,0.332918882369995,PP3;PM1;PM5;PM2,,,"The c.825G>C variant in KCNQ4 is a missense variant predicted to cause substitution of tryptophan by cysteine at amino acid 275 (p.Trp275Cys). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.928, which is above the threshold of 0.7, evidence that correlates with impact to KCNQ4 function (PP3). This variant has been reported in one individual with hearing loss and segregated in an affected first degree relative (SCV000712456.1). This variant is located within the pore-forming intramembrane region (amino acids 271-292) where many variants that cause autosomal dominant hearing loss are located and is defined as a critical functional domain by the ClinGen Hearing Loss VCEP (PM1; PMID: 23717403). A different missense variant at the same codon (p.Trp275Arg) has been classified as Pathogenic by the ClinGen Hearing Loss VCEP (PM5; ClinVar Variation ID 204597, PMID: 25116015). In summary, this variant is classified as Likely Pathogenic for autosomal dominant sensorineural hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM2_Supporting, PP3, PM1, PM5. (VCEP specifications version 2; 10.18.2023)." -NM_000257.3(MYH7):c.1157A>G,PS4;PM1;PM2;PM6;PP3,PM1;PP3;BP4,7.99599170684814,PM1;PP3;PM2,BP4,PM6,PM1;PM2;PP2;PP3;PP5;BP1,0.816510677337647,PP3;PM2;PM1,PS4;PM6,PP5;PP2;BP1,PS4;PM1;PM2;PM6;PP3,0.351853609085083,PM6;PP3;PM2;PM1;PS4,,,"The NM_000257.4(MYH7):c.1157A>G (p.Tyr386Cys) variant has been reported as a de novo occurence in 2 infants with early-onset/severe cardiomyopathy that presented with variable features (1 with features of HCM and RCM, and 1 with features of HCM and LVNC that progressed to DCM; Lakdawala 2012 PMID:22464770; Greenway 2012 PMID:23170025; Alfares 2015 PMID:25611685; LMM pers. comm.) and in an additional case with RCM (age unknown; GeneDx pers. comm.). Collectively, this data meets criteria for PS4_Supporting and PM6. This variant was absent from large population studies (PM2; gnomAD v2.1.1, http://gnomad.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be associated with HCM (PM1; Walsh 2017 PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for complex cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (Kelly 2018 PMID:29300372): PS4_Supporting, PM6, PM2, PM1, PP3." -NM_005343.3(HRAS):c.175G>A,PS4;PM1;PM2;PP1;PP2;PP3,PM1,191.677925348282,PP2;PM1,,PM2;PP3,PM1;PM2;PP3;PP5,0.369871139526367,PP3;PM2;PM1,PS4;PP2;PP1,PP5,PS4;PM1;PM2;PP1;PP2;PP3,0.479533195495605,PP3;PP2;PP1;PM2;PM1;PS4,,,"The c.175G>A (p.Ala59Thr) variant in HRAS has been identified in at least 3 independent occurrences in patients with a RASopathy (PS4_Moderate; GeneDx, Partners LMM, Invitae internal data; ClinVar SCV000198374, SCV000950586). The p.Ala59Thr variant segregated with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Partners LMM internal data). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of HRAS (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ala59Thr variant may impact the protein (PP3). The variant is located in the HRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM1, PM2, PS4_Moderate, PP1, PP2, PP3." -NM_030662.3(MAP2K2):c.400T>C,PS4;PM1;PM2;PP2;PP3,PM1;PP3;BP4,264.390161752701,PP2;PM1;PP3,BP4,PM2,PM1;PM2;PP3;PP5,0.392758131027222,PP3;PM2;PM1,PS4;PP2,PP5,PS4;PM1;PM2;PP2;PP3,0.383073329925537,PP3;PP2;PM2;PM1;PS4,,,"The c.400T>C (p.Tyr134His) variant in MAP2K2 was absent from large population studies (PM2). It has been identified in 3 patients with Cardiofaciocutaneous syndrome and 1 with Noonan syndrome (PS4_Moderate; SCV000063166.5, Hopital Universitaire Robert Debre internal data, PMIDs: 18042262, 27763634)Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K2 (PM1; PMID 29493581). Moreover, a different pathogenic missense variant (p.Tyr134Cys) has been previously identified at this codon of MAP2K2 which may indicate that this residue is critical to the function of the protein (PM5 not met; ClinVar 177868). The variant is located in the MAP2K2 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Tyr134His variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM2, PS4_Moderate, PM1, PP2, PP3." -NM_004333.4(BRAF):c.739T>G,PS4;PM1;PM2;PP2;PP3,PM1;PM5;PP3;BP4,13.155256986618,PP2;PM1;PP3;PM2,PM5;BP4,PS4,PM1;PM2;PP3;PP5,0.371227264404297,PP3;PM2;PM1,PS4;PP2,PP5,PS4;PM1;PM2;PP2;PP3,0.347076892852783,PP3;PP2;PM2;PM1;PS4,,,"The c.739T>G (p.Phe247Val) variant in BRAF has been identified in at least 2 independent occurrences in patients with clinical features of a RASopathy (PS4_Supporting; Partners LMM, GeneDx internal data; GTR Lab IDs 21766, 26957; ClinVar SCV000061624.5, SCV000330320.6). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). A different pathogenic missense variant (p.Phe247Leu) has been previously identified at this codon of BRAF which may indicate that this residue is critical to the function of the protein (PM5 not usable due to PM1 application; ClinVar 180784, 55793). Computational prediction tools and conservation analysis suggest that the p.Phe247Val variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM2, PM1, PP2, PP3." -NM_001754.4(RUNX1):c.316T>A,PS3;PM1;PM2;PP3,,1.46527314186096,PM2,,PM1;PP3,PM1;PM2;PP3;PP5;BP1,0.371410608291626,PP3;PM2;PM1,PS3,PP5;BP1,PS3;PM1;PM2;PP3,0.32424259185791,PP3;PM1;PS3;PM2,,,"The NM_001754.4:c.316T>A (p.Trp106Arg) variant affects one of the residues (AA 105-204) within the RHD (PM1_Supporting). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2). Transactivation assays demonstrating altered transactivation (<20% of wt, and/or reduced to levels similar to well-established pathogenic variants such as R201Q or R166Q) AND data from secondary assay demonstrate altered DNA binding. (PS3; PMID: 25840971). This missense variant has a REVEL score >0.75 (0.976) (PP3). All patients reported in literature with this variant were not confirmed as germline variants (PMID: 21828118, PMID: 19282830, PMID: 25840971). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PS3, PM2, PP3, PM1_supporting." -NM_001754.4(RUNX1):c.314A>C,PS4;PM1;PM2;PM5;PP3,,0.688652515411377,PM5;PP3,,PM1;PM2,PM1;PM2;PP3;PP5;BP1,0.364496469497681,PP3;PM2;PM1,PS4;PM5,PP5;BP1,PS4;PM1;PM2;PM5;PP3,0.3201744556427,PM5;PP3;PM2;PM1;PS4,,,"The NM_001754.4:c.314A>C (p.His105Pro) variant affects one of the residues (AA 105-204) within the RHD (PM1_Supporting). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2). This missense variant has a REVEL score >0.75 (0.953) (PP3). This variant is a missense change at the same residue (p.His105Pro) where a different missense change has been previously established as a likely pathogenic variant (NM_001754.4:c.315C>A (p.His105Glu)) based on MM-VCEP rules for RUNX1 and RNA data or agreement in splicing predictors (SSF and MES) show no splicing effects (PM5_Supporting). This variant has been reported in one proband meeting at least one of the RUNX1-phenotypic criteria (PS4_ Supporting; SCV000807773.1). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM2, PP3, PM1_supporting, PM5_supporting, PS4_supporting." -NM_001754.4:c.315C>A,PS3;PM1;PM2;PP3,,0.717023372650147,PM2;PP3,,PM1;PS3,PM1;PM2;PP3;PP5;BP1,0.364284753799438,PP3;PM2;PM1,PS3,PP5;BP1,PS3;PM1;PM2;PP3,0.311601400375366,PP3;PM1;PS3;PM2,,,"The NM_001754.4:c.315C>A (p.His105Gln) variant affects one of the residues (AA 105-204) within the RHD (PM1_Supporting). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2). Transactivation assays demonstrating altered transactivation (<20% of wt, and/or reduced to levels similar to well-established pathogenic variants such as R201Q or R166Q) AND data from secondary assays demonstrate altered DNA binding and functional consequences in mouse model. (PS3; PMID: 22318203; PMID: 25840971). This missense variant has a REVEL score >0.75 (0.901) (PP3). All patients reported in literature with this variant were not confirmed as germline variants (PMID 22318203, PMID 29722345, PMID 25840971, PMID 24030381, PMID 19282830). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PS3, PM2, PP3, PM1_supporting." -NM_002834.4(PTPN11):c.782T>A,PS4;PM1;PP2,,0.656793832778931,PM1,,PP2,PM1;PM2;PP3;PP5,0.401057004928589,PM1,PS4;PP2,PP3;PP5;PM2,PS4;PM1;PP2,0.317038059234619,PP2;PM1;PS4,,,"The c.782T>A (p.Leu261His) variant in PTPN11 is present in 1/6064 “other” alleles in gnomAD v2.1.1; however, it is absent from gnomAD v3 (PM2 not met). It has been identified in 7 independent occurrences in patients with clinical features of a RASopathy (PS4; PMIDs: 28074573, 22253195, 23756559). A functional assay performed on this variant does not meet approved RASopathy VCEP guidelines for criteria application (PS3 not met; PMID: 28074573). This variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot of PTPN11 (PM1; PMID 29493581). PTPN11 has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant RASopathy based on the RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4, PM1, PP2." -NM_004333.6(BRAF):c.793G>C,PS4;PM1;PM2;PM6;PP2;PP3,,0.633267164230347,PM1;PP3,,PP2;PM2,PM1;PM2;PP3;PP5,0.364014625549316,PP3;PM2;PM1,PS4;PP2;PM6,PP5,PS4;PM1;PM2;PM6;PP2;PP3,0.310089111328125,PM6;PP3;PP2;PM2;PM1;PS4,,,"The c.793G>C (p.Gly265Arg) variant in BRAF was absent from large population studies (PM2; gnomad.broadinstitute.org). It was observed as a de novo occurrence in one proband diagnosed with a RASopathy (PM6, PS4_Supporting; Laboratory for Molecular Medicine internal data, ClinVar SCV000061628.5). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Gly265Arg variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant RASopathy. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM1, PM2, PM6, PP2, PP3." -NM_005633.3(SOS1):c.1276C>A,PS4;PM1;PM2;PP2;PP3,,0.642684936523438,PM2;PP3,,PP2;PM1,PM1;PM2;PP3,0.411989450454712,PP3;PM2;PM1,PS4;PP2,,PS4;PM1;PM2;PP2;PP3,0.332223653793335,PP3;PP2;PM2;PM1;PS4,,,"The c.1276C>A (p.Gln426Lys) variant in SOS1 was absent from large population studies (PM2; gnomad.broadinstitute.org). It was observed in 1 individual with a diagnosis of Noonan syndrome (PS4_Supporting; GeneDx internal data, ClinVar SCV000808402.1). SOS1 has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of SOS1 (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Gln426Lys variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID: 29493581): PM1, PM2, PP2, PP3, PS4_Supporting." -NM_000546.5(TP53):c.396G>C,PS3;PM1;PM2;PP3,,0.727421998977661,PM1;PP3,,PM2;PS3,PM1;PM2;PP3;PP5,0.376925945281982,PP3;PM2;PM1,PS3,PP5,PS3;PM1;PM2;PP3,0.305541515350342,PP3;PM1;PS3;PM2,,,"Transactivation assays show a low functioning allele according to Kato, et al. and there is evidence of a dominant negative effect and loss of function according to Giacomelli, et al. (PS3; PMID: 12826609, 30224644). This variant has a BayesDel score > 0.16 and Align GVGD (Zebrafish) is Class 65 (PP3_Moderate). This variant has >10 observations as a somatic hotspot variant in tumors (PM1; cancerhotspots.org v(2)). This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). In summary, TP53 c.396G>C (p.Lys132Asn) meets criteria to be classified as likely pathogenic for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: PS3, PP3_Moderate, PM1, PM2_Supporting." -NM_001754.4(RUNX1):c.485G>A,PM1;PM2;PM5;PP3,,0.759462118148804,PM2;PP3,,PM1;PM5,PM1;PM2;PP3;PP5;BP1,0.374862909317017,PP3;PM2;PM1,PM5,PP5;BP1,PS4;PM1;PM2;PM6;PP2,0.325146436691284,PM1;PM2,PP2;PM6;PS4,PP3;PM5,"This missense variant has not been reported in gnomAD (v2 and v3) [PM2]. It has been reported as a germline variant by SCV001203102.1 in a proband (70s) with thrombocytopenia and anemia; however, the germline origins were not confirmed in this case and all other reports of the variant (PMID: 19808697, 22689681, 24523240, 24659740, 25592059, 26273060, 27220669, 27534895, 28659335, 28933735, 30373888, 31649132, 32045476, 32208489, COSMIC). The variant is located at a residue that directly contacts DNA (PMID: 11276260, 12377125, 12393679, 12807882, 19808697, 28231333) and is considered a hotspot residue (PMID: 31648317, 27294619, 23958918), especially from a somatic perspective (PMID: 32208489) [PM1]. Although this variant has not been functionally evaluated, computational evidence supports a deleterious effect of this variant [PP3] and another missense variant at the same residue (i.e. p.R162G) is classified as likely pathogenic by the ClinGen MM-VCEP [PM5_supporting]. In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM1, PM2, PM5_supporting, and PP3." -NM_000277.2(PAH):c.1092_1094del,PM2;PM3;PM4;PP4,PM1;PM4,1.44384956359863,PM2;PM4,PM1,PP4,,0,,,,PM1;PM2;PM5;PP3,0.319685697555542,PM2,PP3;PM1;PM5,PM3;PP4;PM4,"The c.1092_1094delTCT variant in PAH has been previously reported as a single variant, found in trans with the Pathogenic variant (per internal PAH ClinGen Working Group classification, see ClinVar allele ID 15635) p.Gly272Ter in one proband with classic PKU (PMID: 1975559); phase was confirmed via parental testing (PM3). Apart from stating that the proband was identified via newborn screening further detail is provided regarding the proband’s phenotype, including whether BH4 deficiency was formally excluded (PP4?). The variant is a protein-length changing variant in a non-repeat region (PM4). It is absent from control databases including ethnically matched individuals, including gnomAD/ExAC, 1000 Genomes, and ESP (PM2)." -NM_000277.2(PAH):c.1092_1106del,PM2;PM3;PM4;PP4,PM1;PM4,1.39032506942749,PM2;PM4,PM1,PM3,,0,,,,PM2;PM3;PM4;PP4,0.324632167816162,PM3;PP4;PM4;PM2,,,"The c.1092_1106del (p.Leu365_Leu369del) variant in PAH has been reported in 1 individual with PKU (PP4; PMID: 1363837) in trans with pathogenic variant p.R408W (PM3). This variant is absent in population databases (PM2). This variant is a 15 bp in-frame deletion in exon 11 (PM4). In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4, PM2, PM3, PM4." -NM_000277.1(PAH):c.208_210delTCT,PS3;PM2;PM3;PM4;PP4,PM1;PM2;PM4,1.38096714019775,PM2;PM4,PM1,PP4,,0,,,,PM2;PM3;PM4;PP4,0.313969135284424,PM3;PP4;PM4;PM2,,PS3,"PAH-specific ACMG/AMP criteria applied: PP4: Phe>120 umol/L with PKU (PMID:25456745); PM3: In trans with: c.842+2T>A (P, ClinGen) (PMID:25456745); PS3: 0% in BioPKU; PM2: Extremely low frequency. ExAC MAF=0.00012; PM4: In frame deletion. In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PP4, PM3, PS3, PM2, PM4)." -NM_000277.2(PAH):c.865G>C,PS1;PM2;PM3;PP3;PP4,PS1;PM1;PP3;BP4,7.5553765296936,PS1;PP3,PM1;BP4,PM2,PM1;PM2;PP3;PP5;BP1,0.359306812286377,PP3;PM2,PS1;PP4;PM3,PP5;BP1;PM1,PS3;PM2;PM3;PM4;PP4,0.320562839508057,PM3;PP4;PM2,PS3;PM4,PP3;PS1,"The c.865G>C (p.Gly289Arg) variant in PAH is absent from population databases and predicted deleterious with in silico prediction software. This is the same amnio acid change as a previously established pathogenic variant (c.865G>A; p.Gly289Arg). It has been identified in trans with a pathogenic variant (R155C, curated by the PAH EP), and a defect in BH4 metabolism was excluded (PMID: 22921945). In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PS1, PM2, PM3, PP3." -NM_004333.4(BRAF):c.735A>T,PS1;PS4;PM1;PM2;PM6;PP2;PP3,PS1;PM1;PP3;BP4,8.01120638847351,PP3;PM1;PS1;PM2,BP4,PP2;PM6,PM1;PM2;PP3;PP5,0.35802173614502,PP3;PM2;PM1,PS1;PS4;PP2;PM6,PP5,PS1;PM2;PM3;PP3;PP4,0.320266723632812,PP3;PS1;PM2,PM3;PP4,PP2;PM1;PM6;PS4,"The c.735A>T p.Leu245Phe variant in BRAF has been identified in at least 2 independent occurrences, one of which was de novo, in patients with clinical features of a RASopathy (PM6, PS4_Supporting; Partners LMM, University Magdeburg internal data; GTR Lab IDs: 21766, 506381 PMID: 19206169, 22190897). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that the p.Leu245Phe variant may impact the protein (PP3). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Of note, the p.Leu245Phe change has also been reported as a consequence of the c.735A>C variant in BRAF, which has been classified as pathogenic and therefore supports that this residue may be critical to protein function (PS1; ClinVar ID: 40347). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM6, PM1, PM2, PS1, PP2, PP3." -NM_005633.3(SOS1):c.1656G>T,PS1;PS2;PS4;PM1;PM2;PP2;PP3,PS1;PM1,14.6982409954071,PM1;PS1;PM2,,PP2;PP3,PM1;PM2;PP3;PP5,0.531394004821777,PP3;PM2;PM1,PS1;PS4;PP2;PS2,PP5,PS1;PS4;PM1;PM2;PM6;PP2;PP3,0.317075967788696,PP3;PP2;PM2;PM1;PS4;PS1,PM6,PS2,"The c.1656G>T (p.Arg552Ser) variant in SOS1 has been reported as a confirmed de novo occurrence in one patient and 2 other probands with clinical features of a RASopathy (PS2, PS4_Moderate; PMID 17586837, 18854871). Of note, one of these cases was an affected mother-child duo (PP1 not met; PMID: 17586837). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). This amino acid residue has been designated as a hotspot. These variants would have received PM5_Strong but the RAS EP decided that PM1 and PM5 cannot be used simultaneously and therefore this rule has been upgraded with expert judgement (PM1_Strong). Of note, the p.Arg552Ser variant in SOS1 has also been a consequence of the c.1656G>C nucleotide change which has been classified as pathogenic (PS1; ClinVar ID 12872). Computational prediction tools and conservation analysis suggest that the p.Arg552Ser variant may impact the protein (PP3). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2, PS1, PM1_Strong, PM2, PS4_Moderate, PP2, PP3." -NM_000277.3(PAH):c.865G>A,PS1;PM2;PM3;PP3;PP4,,0.739319324493408,PP3,,PS1;PM2,PM1;PM2;PP3;PP5;BP1,0.376642465591431,PP3;PM2,PS1;PP4;PM3,PP5;BP1;PM1,PS1;PS2;PS4;PM1;PM2;PP2;PP3,0.318098068237305,PP3;PS1;PM2,PP2;PM1;PS2;PS4,PM3;PP4,"This c.865G>A (p.Gly289Arg) variant in PAH was reported in 2 patients with PAH deficiency (PMID: 27121329) detected with the pathogenic variant p.Gly272* and the likely pathogenic variant p.Arg155Cys. DHPR activity, biopterin and/or pteridine analysis was performed to rule out other causes of hyperphenylalaninemia. This variant has the same amino acid change as a previously established pathogenic variant in ClinVar (Variation ID: 102882). This variant is absent in population databases. Computational evidence for this missense variant supports a deleterious effect. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PS1, PM2, PP4_moderate, PM3, PP3." -NM_000540.2(RYR1):c.1021G>C,PS1;PS3;PS4;PM1;PP1;PP3,,0.776044130325317,PM1;PP3,,PS1;PS3,PM1;PM2;PP3,0.412060976028442,PP3;PM1,PS1;PS4;PS3;PP1,PM2,PS1;PM2;PM3;PP3;PP4,0.306127786636352,PP3;PS1,PM3;PP4;PM2,PP1;PS4;PM1;PS3,"This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions. This sequence variant predicts a substitution of Glycine with Arginine at codon 341 of the RYR1 protein, p.(Gly341Arg), c.1021G>C. This variant was not present in a large population database (gnomAD) at the time this variant was interpreted. This variant has been reported in five unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, four of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (if the proband was unavailable for testing, a positive diagnostic test result in a mutation-positive relative was counted), PS4_Moderate (PMID:12059893, PMID:16163667, PMID:30236257 ). This variant segregates with MHS in five individuals/families, PP1_Moderate (PMID:12059893, PMID:12411788). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:9334205). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, use PM1_Supporting to avoid overweighting with PS1 (PMID: 21118704). Another variant has been assessed as pathogenic occurs at this codon, p.(Gly341Arg, c.1021G>A), PS1. This variant segregates with MHS in two individuals (PMID:12059893). A REVEL score >0.85 (0.876) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as Pathogenic. Criteria implemented: PS4_Moderate, PS3_Moderate, PM1_Supporting, PS1, PP3_Moderate. " -NM_000540.2(RYR1):c.742G>C,PS1;PS3;PS4;PM1;PP1;PP3,,0.693361520767212,PM1;PP3,,PS1;PS3,PM1;PM2;PP3;PP5,0.374715566635132,PP3;PM1,PS1;PS4;PS3;PP1,PP5;PM2,PS1;PS3;PS4;PM1;PP1;PP3,0.33376669883728,PP3;PS3;PP1;PM1;PS4;PS1,,,"This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions.This sequence variant predicts a substitution of glycine with arginine at codon 248 of the RYR1 protein c.742G>C; p.(Gly248Arg). The maximum allele frequency for this variant among the six major gnomAD populations is EAS: 0.00005), a frequency consistent with pathogenicity for MHS. This variant has been reported in four unrelated individuals who have a personal or family history of a malignant hyperthermia reaction and a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted), PS4_Moderate (PMID:30236257, PMID:19346234). This variant segregates with MHS in five individuals/families, PP1_Moderate (PMID:30236257, PMID:19346234, PMID:18564801). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:26115329, PMID:27857962). Another variant assessed as pathogenic occurs at this codon, c.742G>A; p.(Gly248Arg), PS1. This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, use PM1_Supporting to avoid overweighting with PS1 (PMID: 21118704).A REVEL score > 0.85 supports pathogenicity, PP3_Moderate. This variant has been classified as Pathogenic. Criteria implemented: PS4_Moderate, PS3_Moderate, PM1_Supporting, PS1, PP1_Moderate, PP3_Moderate." -NM_001110792.2(MECP2):c.408G>C,PS1;PS3;PM1;PM2;PM6,,0.70138144493103,PM2,,PS1;PM1,PM1;PM2;PP3;BP1,0.38634181022644,PM2;PM1,PS1;PS3;PM6,PP3;BP1,PS1;PS3;PS4;PM1;PP1;PP3,0.346795082092285,PM1;PS3;PS1,PP3;PP1;PS4,PM6;PM2,"The c.372G>C (p.Leu124Phe) variant in MECP2 (NM_004992.3) occurs in the de novo state (biological parentage unconfirmed) in an individual with Rett syndrome (PMID 10991688) (PM6). The c.372G>C (p.Leu124Phe) variant occurs in the well-characterized methyl-DNA binding functional domain of the MECP2 gene (PM1). The c.372G>C (p.Leu124Phe) variant in MECP2 is absent from gnomAD (PM2_supporting). MECP2 heterochromatin binding assay and in vitro transcriptional repression assay have shown that this variant impacts protein function (PMID 12843318) (PS3_supporting). The c.372G>T variant in the MECP2 gene results in a p.Leu124Phe change that is a previously established pathogenic variant (internal database - Invitae) (PS1). In summary, the c.372G>C (p.Leu124Phe) variant in MECP2 is classified as Pathogenic for Rett syndrome based on the ACMG/AMP criteria (PS1, PM1, PM6, PM2_supporting, PS3_supporting)." -NM_001110792.2(MECP2):c.408G>T,PS1;PS2;PM1;PM2,,0.661284685134888,PS1;PM1,,PM2;PS2,PM1;PM2;PP3;BP1,0.358327388763428,PM2;PM1,PS1;PS2,PP3;BP1,PS1;PS3;PM1;PM2;PM6,0.300886869430542,PM1;PS1;PM2,PM6;PS3,PS2,"The c.372G>T (p.Leu124Phe) variant in MECP2 (NM_004992.3) occurs in the mosaic state in a male patient with a neurodevelopmental phenotype consistent with the MECP2 gene (internal database - Invitae) and therefore confirmed to be de novo (PS2). The c.372G>T (p.Leu124Phe) variant occurs in the well-characterized methyl-DNA binding functional domain of the MECP2 gene (PM1). The c.372G>T (p.Leu124Phe) variant in MECP2 is absent from gnomAD (PM2_supporting). The c.372G>C variant in the MECP2 gene results in a p.Leu124Phe change that is a previously established pathogenic variant (PMID 10991688, 12843318) (PS1). In summary, the c.372G>T (p.Leu124Phe) variant in MECP2 is classified as Pathogenic for Rett syndrome based on the ACMG/AMP criteria (PS1, PS2, PM1, PM2_supporting)." -NM_000162.5(GCK):c.523G>A,PS1;PS3;PS4;PM2;PP1;PP2;PP3;PP4,,0.63607668876648,PP2;PM2,,PS1;PS3;PP3,PM1;PM2;PP3,0.405667543411255,PP3;PM2,PP4;PP2;PS3;PS1;PS4;PP1,PM1,PS1;PS2;PM1;PM2,0.31352972984314,PS1;PM2,PS2;PM1,PP3;PS3;PP2;PP1;PS4;PP4,"The c.523G>A variant in the glucokinase gene, GCK causes an amino acid change of Gly to Arg at codon 210 (p.(Gly175Arg)) of NM_000162.5. GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2). This variant is also predicted to be deleterious by computational evidence, with a REVEL score of 0.965, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in 8 unrelated individuals with diabetes (PS4; PMID: 29944009, 20337973, 26552609, internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and three-generation, dominant family history of diabetes/hyperglycemia) (PP4_Moderate; internal lab contributors). This variant segregated with diabetes with 5 informative meioses in 4 families with diabetes (PP1_Strong; internal lab contributors). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, but the wild-type ATP Km is not between 0.4-0.65, and the p.Gly175Arg variant has Kcat/S0.5<0.5 (PS3_Supporting; PMID 10525657). The nucleotide change c.523G>C, which causes the same amino acid change, has been classified as pathogenic for MODY by the ClinGen MDEP (PS1). In summary, this variant meets the criteria to be classified as Pathogenic for GCK-MODY. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0, approved 6/7/2023) : PS4, PP1_Strong, PP4_Moderate, PS3_Supporting, PM2_Supporting, PP2, PP3, PS1." -NM_000277.1(PAH):c.782G>C,PM2;PM3;PM5;PP3;PP4,,0.722711801528931,PM2,,PM5;PP3,PM1;PM2;PP3;PP5;BP1,1.38493967056274,PP3;PM2,PM5;PP4;PM3,PP5;BP1;PM1,PS1;PS3;PS4;PM2;PP1;PP2;PP3;PP4,0.31301736831665,PP3;PP4;PM2,PS3;PP2;PP1;PS4;PS1,PM3;PM5,"The PAH c.782G>C (p.Arg261Pro) variant has been reported in multiple affected individuals (PMID: 26666653, Bh4 deficiency not ruled out, PP4). It has been detected with 5 known pathogenic variants (PM3_S). It is absent from ExAC/gnomAD. Computational evidence supports a deleterious effect. Also, p.R261Q is interpreted as pathogenic. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM3_S, PM2, PM5, PP4, PP3." -NM_000277.2(PAH):c.734T>C,PM3;PM5;PP4,PM1;PM2;PM5;PP3;BP4,7.8391854763031,PM5,PM1;BP4;PP3;PM2,PP4,PM1;PM2;PP3;PP5;BP1,0.376780271530151,,PM5;PP4;PM3,PP5;PM1;BP1;PP3;PM2,PM2;PM3;PM5;PP3;PP4,0.310577154159546,PM3;PM5;PP4,PP3;PM2,,"PAH-specific ACMG/AMP criteria applied: PM5: V245L Pathogenic; PP4_Moderate: Seen in at least 7 MHP patients. Exclusion of a defect in tetrahydrobiopterin metabolism. Upgraded per ClinGen Metabolic Workgroup. (PMID:7981714; PMID:9298832; PMID:9634518); PM3_VeryStrong: V245A detected with IVS-12nt1, R252W, L194P (both P/LP), R408W (Path). Upgraded per ClinGen SVI Workgroup (PMID:7981714; PMID:9298832; PMID:8088845). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM5, PP4_Moderate, PM3_VeryStrong)." -NM_000257.3(MYH7):c.2221G>T,PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5,7.95476245880127,PM1;PM5;PP3,,PM2;PP1,PM1;PM2;PP2;PP3;PP5;BP1,0.370798349380493,PP3;PM2;PM1,PS4;PM5;PP1,PP5;PP2;BP1,PM3;PM5;PP4,0.306227684020996,PM5,PM3;PP4,PP3;PP1;PM2;PM1;PS4,"The c.2221G>T (p.Gly741Trp) variant in MYH7 has been reported in >15 individuals with hypertrophic cardiomyopathy (PS4; PMID: 8533830; PMID:15856146; PMID:27532257; Partners LMM ClinVar SCV000203910.4; AGCMC Sydney ClinVar SCV000212638.1). This variant segregated with disease in 5 affected individuals (PP1_Moderate; PMID:15856146; AGCMC Sydney ClinVar SCV000212638.1). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2221G>C p.Gly741Arg - Variation ID 14098). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PM1; PM2; PM5; PP1_Moderate; PP3" -NM_000257.3(MYH7):c.2221G>C,PS4;PM1;PM2;PM5;PM6;PP1;PP3,PM1;PM5,7.46528601646423,PP3;PM1;PM5,,PM2;PP1,PM1;PM2;PP2;PP3;PP5;BP1,0.363935708999634,PP3;PM2;PM1,PS4;PM5;PM6;PP1,PP5;PP2;BP1,PS4;PM1;PM2;PM5;PP1;PP3,0.287145614624023,PM5;PP3;PP1;PM2;PM1;PS4,,PM6,"The c.2221G>C (p.Gly741Arg) variant in MYH7 has been reported in >12 individuals with hypertrophic cardiomyopathy (PS4; PMID:8483915; PMID:15563892; PMID:20031618; PMID:15358028; Partners LMM ClinVar SCV000059430.5; SHaRe consortium, PMID: 30297972). This variant has been identified as a de novo occurrence in 1 proband with hypertrophic cardiomyopathy (PM6; PMID:15563892). This variant segregated with disease in 3 affected individuals (PP1; PMID:8483915; Partners LMM ClinVar SCV000059430.5). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2221G>T p.Gly741Trp - Variation ID 177665). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PM1; PM2; PM5; PM6; PP1; PP3" -NM_000257.3(MYH7):c.2167C>T,PS4;PM1;PM2;PM5;PM6;PP1;PP3;BP2,PM1;PM2;PM5,8.01106882095337,PM1;PM5;PM2,,PM6;PP3,PS3;PM1;PM2;PP2;PP3;PP5;BP1,0.370083808898926,PP3;PM2;PM1,PM5;PM6;PS4;PP1;BP2,PP5;PP2;PS3;BP1,PS4;PM1;PM2;PM5;PM6;PP1;PP3,0.311627149581909,PM6;PM5;PP3;PP1;PM2;PM1;PS4,,BP2,"The c.2167C>T (p.Arg723Cys) variant in MYH7 has been reported in >20 individuals with hypertrophic cardiomyopathy (PS4; PMID:1430197; PMID:27532257; PMID:9829907; PMID:16199542; PMID:20359594; PMID:12707239; Partners LMM ClinVar SCV000059423.5; AGCMC Sydney ClinVar SCV000212630.1). Five of these probands carried additional variants in sarcomere genes (BP2; PMID:20359594; PMID:12707239; Partners LMM ClinVar SCV000059423.5). This variant has been identified as a de novo occurrence in 1 proband with hypertrophic cardiomyopathy (PM6; PMID:1430197). This variant segregated with disease in 7 affected individuals (PP1_Strong; PMID:9829907; Partners LMM ClinVar SCV000059423.5; AGCMC Sydney ClinVar SCV000212630.1). This variant was identified in 2/66738 European chromosomes (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2167C>G p.Arg723Gly - ClinVar Variation ID 42885). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. The benign evidence code BP2 was not considered to be in conflict with this conclusion given that presence of a second variant can be seen in individuals with cardiomyopathy and may contribute to the severity of disease. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_ Strong; PM1; PM2; PM5; PM6; PP3; BP2" -NM_000257.3(MYH7):c.2167C>G,PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5,7.95137643814087,PM1;PM5,,PM2;PP3,PM1;PM2;PP2;PP3;PP5;BP1,0.38297176361084,PM1;PM2;PP3,PS4;PM5;PP1,PP2;BP1;PP5,PS4;PM1;PM2;PM5;PM6;PP1;PP3;BP2,0.292257785797119,PM5;PP3;PP1;PM2;PM1;PS4,PM6;BP2,,"The c.2167C>G (p.Arg723Gly) variant in MYH7 has been reported in 12 individuals with hypertrophic cardiomyopathy (PS4; PMID:11113006; PMID:19150014; PMID:17097032; Partners LMM ClinVar SCV000059422.5; SHaRe consortium, PMID: 30297972). This variant segregated with disease in >20 affected individuals (PP1_Strong; PMID:11113006). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2167C>T p.Arg723Cys - ClinVar Variation ID 14095). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_ Strong; PM1; PM2; PM5; PP3" -NM_000257.3(MYH7):c.2156G>A,PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5,7.87559461593628,PM1;PM5,,PM2;PP3,PM1;PM2;PP2;PP3;PP5;BP1,0.430699110031128,PM1;PM2;PP3,PS4;PM5;PP1,PP2;BP1;PP5,PS4;PM1;PM2;PM5;PP1;PP3,0.335282564163208,PM5;PP3;PP1;PM2;PM1;PS4,,,"The c.2156G>A (p.Arg719Gln) variant in MYH7 has been reported in >30 individuals with hypertrophic cardiomyopathy (PS4; PMID:7848441; PMID:16199542; PMID:15358028; PMID:18411228; Partners LMM ClinVar SCV000059421.5; AGCMC Sydney ClinVar SCV000212634.1; SHaRe consortium, PMID: 30297972). This variant segregated with disease in 7 affected individuals (PP1_Strong; PMID:7848441; Partners LMM ClinVar SCV000059421.5). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2155C>T p.Arg719Trp ClinVar Variation ID 14104). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_ Strong; PM1; PM2; PM5; PP3" -NM_000257.3(MYH7):c.1208G>A,PS3;PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5,1472.01292085648,PP3;PM1;PM5,,PM2;PP1,PM1;PM2;PP2;PP3;PP5;BP1,0.392212629318237,PM1;PM2;PP3,PS4;PM5;PP1;PS3,PP2;BP1;PP5,PS4;PM1;PM2;PM5;PP1;PP3,0.335064649581909,PM5;PP3;PP1;PM2;PM1;PS4,,PS3,"The c.1208G>A (p.Arg403Gln) variant in MYH7 has been reported in >30 individuals with hypertrophic cardiomyopathy and segregated with disease in >30 affected family members (PS4 and PP1_Strong; PMID:1638703; PMID:1975517; PMID:7789380; PMID:12975413; PMID:24268868; PMID:10725281; PMID:20800588; PMID:12707239; PMID:27532257; AGCMC Sydney ClinVar SCV000692503.1; Invitae ClinVar SCV000253815.4; Partners LMM ClinVar SCV000059359.5; SHaRe consortium, PMID: 30297972). Mouse model indicates that this variant disrupts the function of MYH7 and leads to a phenotype consistent with HCM (PS3: PMID:8614836). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.1207C>T (p.Arg403Trp) - Variation ID 14102). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS3; PS4; PP1_ Strong; PM1; PM2; PM5; PP3" -NM_000257.3(MYH7):c.1207C>T,PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5;PP3;BP4,7.6662495136261,PP3;PM1;PM5;PM2,BP4,PP1,PM1;PM2;PP2;PP5;BP1,0.383901357650757,PM2;PM1,PS4;PM5;PP1;PP3,PP2;BP1;PP5,PS3;PS4;PM1;PM2;PM5;PP1;PP3,0.299535274505615,PM5;PP3;PP1;PM2;PM1;PS4,PS3,,"The c.1207C>T (p.Arg403Trp) variant in MYH7 has been reported in >20 individuals with hypertrophic cardiomyopathy and segregated with disease in >20 affected family members (PS4 and PP1_Strong; PMID:1052196; PMID:7662452; PMID:7848420; PMID:8254035; PMID:8268932; PMID:12707239; PMID:12974739; PMID:15010274; PMID:15856146; PMID:17612745; PMID:20428263; PMID:21239446; PMID:26383716; Partners LMM ClinVar SCV000059358.5; AGCMC Sydney ClinVar SCV000212643.1; SHaRe consortium, PMID: 30297972). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.1208G>A p.Arg403Gln - Variation ID 14087). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_Strong; PM1; PM2; PM5; PP3" -NM_000257.3(MYH7):c.1358G>A,PS4;PM1;PM2;PM5;PM6;PP3,PM1;PM5,7.4386739730835,PM1;PM5;PM2,,PS4;PP3,PM1;PM2;PP2;PP3;PP5;BP1,0.402814388275147,PM1;PM2;PP3,PS4;PM5;PM6,PP2;BP1;PP5,PS4;PM1;PM2;PM5;PP1;PP3,0.315271615982056,PM5;PP3;PM2;PM1;PS4,PP1,PM6,"The c.1358G>A (p.Arg453His) variant in MYH7 has been reported in >12 individuals with hypertrophic cardiomyopathy (PS4; PMID:27532257; PMID:20428263; PMID:15858117; PMID:20800588; PMID:21835320; PMID:22429680; Partners LMM ClinVar SCV000059369.5; Invitae ClinVar SCV000253816.4; SHaRe consortium, PMID: 30297972). This variant was been identified as a de novo occurrence in 1 proband with hypertrophic cardiomyopathy (PM6; PMID:20428263). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.1357C>T p.Arg453Cys; ClinVar Variation ID 14089). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PM1; PM2; PM5; PM6; PP3" -NM_002880.3(RAF1):c.775T>A,PS3;PS4;PM1;PM2;PM5;PM6;PP1;PP2;PP3,PM1;PM5,8.5560519695282,PP2;PP3;PM1;PM5,,PM2;PS3;PS4,PM1;PM2;PP3;PP5,0.374517202377319,PM1;PM2;PP3,PP2;PP1;PS3;PS4;PM5;PM6,PP5,PS4;PM1;PM2;PM5;PM6;PP3,0.330689191818237,PM6;PM5;PP3;PM2;PM1;PS4,,PP2;PP1;PS3,"The c.775T>A (p.Ser259Thr) variant in RAF1 has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; APHP-Robert Debré Hospital internal data; GTR ID's: 28338). The p.Ser259Thr variant has been identified in at least 8 independent occurrences in patients with a RASopathy (PS4_Supporting; GeneDx, Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 21766, 506381 PMID: 21784453; ClinVar SCV000061360.5; SCV000209017.10). The p.Ser259Thr variant in RAF1 has been reported to segregate with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 506381; ClinVar SCV000209017.9). In vitro functional studies provide some evidence that the p.Ser259Thr variant may impact protein function (PS3; PMID: 21784453, 20052757). At least 2 other pathogenic missense variants have been previously identified at this codon of RAF1 which may indicate that this residue is critical to the function of the protein (PM5_Strong; ClinVar 40603, 40602, 228288). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of RAF1 (PM1; PMID 29493581). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ser259Thr variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6_Strong, PS4_Supporting, PP1, PM5_Strong, PM2, PM1, PP2, PP3, PS3." -NM_004985.4(KRAS):c.101C>T,PS2;PM2;PM5;PP2;PP3,PM5;PP3;BP4,16.2139370441437,PP2;PM5;PP3;PM2,BP4,PS2,PM1;PM2;PP3;PP5,0.396968364715576,PM2;PP3,PP2;PM5;PS2,PP5;PM1,PS3;PS4;PM1;PM2;PM5;PM6;PP1;PP2;PP3,0.283566236495972,PP3;PP2;PM5;PM2,PM6;PS3;PP1;PM1;PS4,PS2,"The c.101C>T (p.Pro34Leu) variant in KRAS has been reported as a confirmed de novo occurrence in a patient with clinical features of a RASopathy (PS2; PMID 17056636, 20949621). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). A different pathogenic missense variant has been previously identified at this codon of KRAS which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 12590). Computational prediction tools and conservation analysis suggest that the p.Pro34Leu variant may impact the protein (PP3; PMID: 24803665). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PS2, PM2, PM5, PP3, PP2." -NM_002755.3(MAP2K1):c.388T>C,PS4;PM2;PM5;PM6;PP2;PP3,PM1;PM5;PP3;BP4,2686.98474836349,PM5;PP3,PM1;BP4,PP2;PM2,PM1;PM2;PP2;PP3;PP5,0.485947132110596,PP2;PM2;PP3,PS4;PM5;PM6,PP5;PM1,PS2;PM2;PM5;PP2;PP3,0.37100625038147,PP3;PP2;PM5;PM2,PS2,PM6;PS4,"The c.388T>C (p.Tyr130His) variant in MAP2K1 has been reported as an unconfirmed de novo occurrence in two probands with clinical features of a RASopathy (PM6_Strong; PMID: 1915617, Ambry Genetics internal data, ClinVar SCV000740998.1). One of these patients had a clinical diagnosis of cardiofaciocutaneous syndrome (PS4_Supporting). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The variant is located in the MAP2K1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). The variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K1 (PM1 not applied; PMID 29493581). Moreover, a different pathogenic missense variant has been previously identified at this codon of MAP2K1 which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 13351). Computational prediction tools and conservation analysis suggest that the p.Tyr130His variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM6_Strong, PM5, PM2, PP2, PP3." -NM_000540.3(RYR1):c.1840C>T,PS3;PS4;PM5;PP1;PP3;BS2,,0.976229429244995,PM5;PP3,,PP1;BS2,PM1;PM2;PP3,0.397022247314453,PP3,PP1;PS3;PS4;PM5;BS2,PM2;PM1,PS4;PM2;PM5;PM6;PP2;PP3,0.328364372253418,PP3;PS4;PM5,PP2;PM6;PM2,PP1;PS3;BS2,"This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions.This sequence variant predicts a substitution of Arginine with Cysteine at codon 614 of the RYR1 protein, p.(Arg614Cys). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.00019, a frequency consistent with pathogenicity for MHS. This variant has been reported in over 100 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, over 100 of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (if the proband was unavailable for testing, a positive diagnostic test result in a mutation-positive relative was counted), PS4 (PMID:24433488, PMID:16163667, PMID:30236257, and others). This variant has been identified in an individual with negative IVCT/CHCT results, BS2_Moderate (PMID:10484775). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:26115329). This variant does not reside in a hotspot for pathogenic variants that contribute to MHS (PMID: 21118704). Another variant that has been assessed as pathogenic occurs at this codon, p.(Arg614Leu), PM5 (PMID:16917943). p.(Arg614Cys) segregates with MHS in 38 individuals PP1_Strong, (PMID:25960145, PMID:7586638, PMID:11493496 and others). A REVEL score >0.85 supports a pathogenic status for this variant, PP3_Moderate. Criteria implemented: PS3_Moderate, PS4, PM5, PP1_Strong, PP3_Moderate, BS2_Moderate. Based on using Bayes to combine criteria this variant is assessed as Pathogenic, (PMID: 29300386)." -NM_000540.3(RYR1):c.6487C>T,PS3;PS4;PM1;PM5;PP1;PP3;BS2,,0.903173446655273,PM1;PM5;BS2,,PS3;PS4;PP3,PM1;PM2;PP3,0.413597583770752,PM1;PP3,PP1;PS3;PS4;PM5;BS2,PM2,PS3;PS4;PM5;PP1;PP3;BS2,0.315521240234375,PM5;PP3;PS3;BS2;PP1;PS4,,PM1,"This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions.This sequence variant predicts a substitution of Arginine with Cysteine at codon 2163 of the RYR1 protein, p.(Arg2163Cys). The maximum allele frequency for this variant among the six major gnomAD populations is SAS: 0.000033, a frequency consistent with pathogenicity for MHS. This variant has been reported in three unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, three of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (if the proband was unavailable for testing, a positive diagnostic test result in a mutation-positive relative was counted), PS4_Moderate (PMID:10484775, PMID:30236257, PMID:9497245). This variant has been identified in an individual with a negative IVCT/CHCT result, BS2_Moderate. Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:9873004). Another variant has been assessed as pathogenic at this codon, p.(Arg2163His), PM5 (PMID:30236257 ). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, use PM1_Supporting to avoid overweighting with PM5 (PMID: 21118704). This variant segregates with MHS in over 15 individuals PP1_Strong, (PMID:9497245, PMID:30236257, PMID:10484775). A REVEL score >0.85 supports a pathogenic status for this variant, PP3_Moderate. Based on using Bayes to combine criteria this variant is assessed as Pathogenic, (PMID: 29300386). Criteria implemented: PS3_Moderate, PS4_Moderate, PM1_Supporting, PM5, PP1_Strong, PP3_Moderate, BS2_Moderate." -NM_003159.2(CDKL5):c.215T>C,PS3;PS4;PM2;PM5;PM6;PP3,,0.900096416473389,PP3,,PM5;PM2,PM1;PM2;PP2;PP3;PP5,0.433248281478882,PM2;PP3,PS4;PM5;PM6;PS3,PP2;PP5;PM1,PS3;PS4;PM1;PM5;PP1;PP3;BS2,0.328516960144043,PP3;PS3;PS4;PM5,PP1;PM1;BS2,PM6;PM2,"The p.Ile72Thr variant in CDKL5 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with CDKL5 disease (PMID 19396824, 19241098) (PM6). The p.Ile72Thr variant in CDKL5 has been reported in at least 3 other individuals with CDKL5 disease (PMID 19396824, 19241098, 25657822, ClinVar) (PS4_moderate). The p.Ile72Thr variant in CDKL5 is absent from gnomAD (PM2). Multiple likely pathogenic missense variants have been previously identified within this codon (p.Ile72Asn; p.Ile72Met) which indicates that this residue is critical to the function of the protein (PMID 28074849, 27779742, 16015284) (PM5_strong). Phosphoproteomic screening of the cellular substrates of CDKL5 (MAP1S, CEP131 and DLG5) has shown that the p.Ile72Thr variant impacts protein function (PMID 30266825) (PS3_supporting). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own(PP3). In summary, the p.Ile72Thr variant in CDKL5 is classified as Pathogenic for CDKL5 disease based on the ACMG/AMP criteria (PM5_strong, PM6, PS4_moderate, PS3_supporting, PM2_supporting, PP3)." -NM_001323289.1:c.59G>T,PS2;PM1;PM2;PM5;PP3,PM1;PM5;PP3;BP4,7.76839661598206,PM1;PM5;PP3,BP4,PM2,PM1;PM2;PM5;PP2;PP3,0.394157886505127,PP3;PM1;PM2;PM5,PS2,PP2,PS3;PS4;PM2;PM5;PM6;PP3,0.366951942443848,PP3;PM5;PM2,PM6;PS4;PS3,PS2;PM1,"The p.Gly20Val variant in CDKL5 occurs in the de novo state (biological parentage confirmed) in this individual (PS2). Multiple pathogenic missense variants have been previously identified within this codon which indicates that this residue is critical to the function of the protein (PMID 23064044, 20397747) (PM5_Strong). The p.Gly20Val variant in CDKL5 is absent from gnomAD (PM2_Supporting). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own (PP3). In summary, the p.Gly20Val variant in CDKL5 is classified as pathogenic for CDKL5-associated disorder based on the ACMG/AMP criteria (PS2, PM5_strong, PM2_supporting, PP3)." -NM_014297.5(ETHE1):c.488G>A,PS3;PM3;PM5;PP3;PP4,PM1;PM2;PM5;PP3;BP4,131.541824579239,PM5;PP3,PM1;BP4;PM2,PM3,PM1;PM2;PP3;PP5,0.372634172439575,PP3,PM5;PS3;PM3;PP4,PM1;PM2;PP5,PS2;PM1;PM2;PM5;PP3,0.338687181472778,PP3;PM5,PS2;PM1;PM2,PM3;PP4;PS3,"The c.488G>A (NM_014297.5) variant in ETHE1 is a missense variant predicted to cause substitution of arginine by glutamine at amino acid 163 (p.R163Q). The highest population minor allele frequency for this variant in gnomAD v2.1.1 is 0.00005 (13/251,458 alleles) in the general population, which is higher than the ClinGen ETHE1 threshold < 0.00002 for PM2, thus it does not meet this criterion. This variant was originally reported in two compound heterozygous (c.131_132delAG; p. E44fsX105) relatives who both had developmental delay, petechiae, orthostatic acrocyanosis, chronic diarrhea, and ethylmalonic aciduria which is a phenotype highly specific to ethylmalonic encephalopathy (PP4_moderate; PMID: 14732903). This variant has been detected in at least 9 patients reported in the literature with ethylmalonic encephalopathy, however, many of the cases are not scoreable according to the SVI recommendation for in trans criterion for PM3, as parental phasing was not performed or the second variant was a VUS (PMID: 18593870; PMID: 16183799, PMID: 30298498). After review of scoreable cases, it was determined by the ETHE1 VCEP that four reported cases were scorable. A single relative from family L from PMID: 14732903 was awarded 1.0 as this patient was a compound heterozygote for an upstream truncating variant (c.131_132delAG; p. E44fsX105), which was confirmed in trans by segregation analysis. Additionally, while the p.E44fsX105 has not been formally curated at this time, given that the p.E44fsX105 is a truncating variant that is predicted to undergo nonsense mediated decay, it is also a strong candidate for a pathogenic classification; the VCEP agreed that this was justification to score this case as 1.0. Patients reported in PMID: 22020834 and PMID: 27771676 were each awarded 0.25 for their respective VUS’s, which were also confirmed in trans. A homozygous patient reported in PMID: 27391121 in whom homozygosity was confirmed via trio WES including parental samples was scored 0.5. This was confirmed by Baylor Genetics who performed the testing for this study (PM3_Strong; Total score- 2.0). ETHE1 encodes persulfide dioxygenase. Persulfide dioxygenase activity measured in recombinant human ETHE1 proteins (both wild-type and p.R163Q) expressed in E.Coli (purified to homogeneity) showed that the p.R163Q recombinant E.Coli only exhibited ~10% of wild-type catalytic activity, indicating that this variant impacts protein function (PS3_supporting; PMID: 25198162). One other missense variant [c.487C>T, p.R163W; PMID 14732903, PMID 16828325, PMID 16183799, PMID 28698729; ClinVar Variation ID: 2317], in the same codon has been classified as pathogenic for ethylmalonic encephalopathy by the ClinGen ETHE1 VCEP (PM5). The computational predictor [REVEL] gives a score of 0.928, which is above the threshold of 0.75, evidence that correlates with impact on ETHE1 function (PP3). In summary, this variant meets the criteria to be classified as pathogenic for Autosomal Recessive Ethylmalonic Encephalopathy. ACMG/AMP criteria applied, as specified by the ClinGen ETHE1 VCEP (version 1.0): PM3_strong, PP4_Moderate, PS3_supporting, PM5, PP3. Approved 7/12/2021." -NM_000257.4(MYH7):c.2710C>T,PS4;PM2;PM5;PM6;PP1;PP3,PM1;PM2;PM5,7.78034257888794,PM5;PP3;PM2,PM1,PP1;PS4,PS3;PM1;PM2;PP2;PP3;BP1,0.371264696121216,PP3;PM2,PM6;PS4;PP1;PM5,PS3;PM1;PP2;BP1,PS3;PM3;PM5;PP3;PP4,0.336124420166016,PP3;PM5,PM3;PP4;PS3,PP1;PM6;PS4;PM2,"The NM_000257.4:c.2710C>T (p.Arg904Cys) variant in MYH7 has been identified in 4 individuals with DCM in the literature (1 of whom also had LVNC; van Spaendonck-Zwarts 2013 PMID:23349452; van der Zwaag 2011 PMID:20573160; Walsh 2017 PMID:27532257; Miller 2017 PMID29212898) and 3 individuals with LVNC (2 of which were pediatric; Yang 2014 PMID:25326635; Wang 2017 PMID:28855170; van Waning 2018 PMID:29447731). This variant was identified in 8 individuals with DCM and 1 proband with LVNC by clinical laboratories (GeneDx pers. comm.; Invitae pers. comm.; LMM pers. comm.; OMGL pers comm.). Only probands with DCM are counted towards PS4 (n=12; PS4_Moderate). This variant segregated with DCM in 15 affected individuals from 4 families (PP1_Strong; van der Zwaag 2011 PMID:20573160; GeneDx pers. comm.; LMM pers. comm.; OMGL pers. comm.) and was assumed de novo in 1 of the above cases (PM6; GeneDx pers. comm.). This variant has been identified in 0.010% (1/10080) of Ashkenazi Jewish chromosomes by gnomAD v2.1.1 (https://gnomad.broadinstitute.org), but was absent from all other populations. A different pathogenic missense variant has been previously identified at this codon, which indicates that this residue may be critical to the function of the protein (PM5; c.2711G>A p.Arg904His - Variation ID 42926). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for dilated cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (Kelly 2018 PMID:29300372): PS4_Moderate, PP1_Strong, PM6, PM2, PM5, PP3." -NM_004958.4(MTOR):c.4448G>A,PS2;PS4;PM1;PM2;PM5;PP2,PM1;PM5;PP3;BP4,13.0135538578033,PP2;PM1;PM5,BP4;PP3,PM2;PS2,PM1;PM2;PP3;PP5,0.388700723648071,PM1;PM2,PS4;PP2;PS2;PM5,PP3;PP5,PS4;PM2;PM5;PM6;PP1;PP3,0.321320533752441,PS4;PM5;PM2,PP3;PP1;PM6,PP2;PM1;PS2,"The c.4448G>A (NM_004958.4) variant in MTOR is a missense variant predicted to cause substitution of (p.Cys1483Tyr). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). MTOR, in which the variant was identified, is defined by the ClinGen Brain Malformations Expert Panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). A different amino acid change (p.Cys1483Arg), at this locus is classified as pathogenic for Overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes by the ClinGen BMEP (PM5). This variant resides within the kinase domain of MTOR that is defined as a critical functional domain by the ClinGen BMEP (PMIDs: 23322780, 27482884, 21210909) (PM1_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4; PMIDs: 22729223; 28892148; 25599672; 26619011; identified in 2 individuals with neuroimaging demonstrating at least one large cerebral hemisphere with cortical malformation(s), 1 individual with macrocephaly ( >=2 SD) and Developmental Delay or Intellectual disability without cortical malformations, it has been shown to demonstrate an increase cell growth phenotype in patient cell lines and at least 3 tumor samples in the literature and COSMIC). This variant has been confirmed de novo and has been identified with variable allelic fractions consistent with a post-zygotic event (PS2_Strong; PMID: 28892148). In summary, this variant meets the criteria to be classified as Pathogenic for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: PM2_P, PP2, PM5, PM1_P, PS4, PS2; 13 points(VCEP specifications version 1; Approved: 1/31/2021)" -NM_004958.3:c.5930C>G,PS2;PS3;PS4;PM1;PM2;PM5;PP2,,4.40990972518921,PM1;PM5,,PP2;PM2;PS3,PM1;PM2;PM5;PP3,0.407511234283447,PM1;PM2;PM5,PS3;PP2;PS2;PS4,PP3,PS2;PS4;PM1;PM2;PM5;PP2,0.321476936340332,PM5;PP2;PM2;PS2;PM1;PS4,,PS3,"The c.5930C>G (NM_004958.4) variant in MTOR is a missense variant predicted to cause substitution of (p.Thr1977Arg). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). MTOR, in which the variant was identified, is defined by the ClinGen Brain Malformations Expert Panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). A different amino acid change (p.Thr1977Lys), at this locus is classified as pathogenic for Overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes by the ClinGen BMEP (PM5). This variant resides within the kinase domain of MTOR that is defined as a critical functional domain by the ClinGen BMEP (PMIDs: 23322780, 27482884, 21210909) (PM1_Supporting). This variant has been shown to significantly increase phosphorylation levels in experiments with case and controls cells of similar isogenic backgrounds indicating that this variant impacts protein function (PMID: 24631838) (PS3_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_M; PMIDs: 25799227, 29281825, identified in 2 individuals with neuropathology confirmatory of a malformation of cortical development, 1 individual with neuroimaging appearance consistent with a malformation of cortical development (without neuropathology), 5 tumor samples in the literature and COSMIC). Testing of unaffected and affected tissue show variable allelic fractions consistent with a post-zygotic event (PS2_Moderate; PMID: 25799227). In summary, this variant meets the criteria to be classified as Pathogenic for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: PM2_P, PP2, PM5, PM1_P, PS3_P, PS4_M, PS2_M; 10 points (VCEP specifications version 1; Approved: 1/31/2021)" -NM_002880.3(RAF1):c.769T>C,PS4;PM2;PM6;PP2,,0.712877035140991,PM2,,PP2;PM6,PM1;PM2;PP3;PP5,0.365538358688354,PM2,PM6;PS4;PP2,PP3;PP5;PM1,PS2;PS3;PS4;PM1;PM2;PM5;PP2,0.328930139541626,PP2;PS4;PM2,PS2;PM1;PS3;PM5,PM6,"The c.769T>C (p.Ser257Pro) variant in RAF1 was absent from large population studies (PM2; gnomAD.broadinstitute.org). It has been identified in 3 patients with clinical features of a RASopathy (PS4_Moderate, SCV000206160.5; SCV000209015.10; PMID 23321623). In one proband the variant occurred de novo without parental confirmation (PM6). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 13957) Furthermore, the p.Ser257Pro variant is located in RAF1, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM1, PM2, PM6, PP2." -NM_005343.3(HRAS):c.175G>A,PS4;PM1;PM2;PP1;PP2;PP3,,0.676827907562256,PP2;PM1;PP3,,PM2;PP1,PM1;PM2;PP3;PP5,0.399978876113892,PP3;PM2;PM1,PS4;PP2;PP1,PP5,PS4;PM2;PM6;PP2,0.329801321029663,PP2;PS4;PM2,PM6,PP3;PP1;PM1,"The c.175G>A (p.Ala59Thr) variant in HRAS has been identified in at least 3 independent occurrences in patients with a RASopathy (PS4_Moderate; GeneDx, Partners LMM, Invitae internal data; ClinVar SCV000198374, SCV000950586). The p.Ala59Thr variant segregated with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Partners LMM internal data). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of HRAS (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ala59Thr variant may impact the protein (PP3). The variant is located in the HRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM1, PM2, PS4_Moderate, PP1, PP2, PP3." -NM_005633.3(SOS1):c.1018C>T,PP2;BS1;BS4;BP5,,0.686291694641113,PP2,,BS4;BS1,PM1;PM2;PP3;BP6;BS2,0.363005638122559,,BS4;BP5;PP2;BS1,PM1;BS2;BP6;PP3;PM2,PS4;PM1;PM2;PP1;PP2;PP3,0.335641622543335,PP2,PP3;PP1;PM2;PM1;PS4,BS1;BP5;BS4,"The c.1018C>T (p.Pro340Ser) variant in the SOS1 gene has been found not to segregate in a family member of a patient who underwent testing for RASopathies as well as another adult who was unaffected (BS4; GeneDx, Invitae internal data; GTR Lab ID: 26957, 500031; SCV000514724.5, SCV000659124.2). This variant has also been identified in a patient with an alternate molecular basis of disease (BP5; PMID 22585553). The filtering allele frequency of the p.Pro340Ser variant is 0.022% for East Asian exomes in the gnomAD database (20/251276 with 95% CI), which is high enough frequency to be considered strong evidence for the variant being benign by the ClinGen RASopathy Expert Panel (BS1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BS4, BP5, BS1." -NM_002880.3(RAF1):c.94A>G,PP2;BS1;BS2;BP4;BP5,,0.663318634033203,BS1;BS2,,PP2;BP4,PM1;BP6,0.355585336685181,,BP4;BS2;PP2;BS1;BP5,PM1;BP6,PP2;BS1;BS4;BP5,0.307804107666016,PP2;BS1;BP5,BS4,BP4;BS2,"The c.94A>G (p.Ile32Val) variant in the RAF1 gene has been identified in patients who underwent testing for a RASopathy, however it has also been identified in multiple adults who did not have clinical features of a RASopathy (BS2, BP5; Invitae, EGL Diagnostics, GeneDx internal data; GTR Lab ID: 500031, 500060; SCV000287747.4, SCV000227277.5, SCV000209002.14). The filtering allele frequency of the p.Ile32Val variant is 0.017% for European (non-Finnish) genomes in the gnomAD database (8/31404 with 95% CI) which is a high enough frequency to be considered strong evidence that the variant is benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BS1). Computational prediction tools and conservation analysis suggest that the p.Ile32Val variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BS2, BP5, BS1, BP4." -NM_000314.6(PTEN):c.520T>A,PS3;PM2;PP2,,0.683493375778198,PP2,,PM2,PM1;PM2;PP3;PP5;BP1,0.369442939758301,PM2,PS3;PP2,PP3;PM1;PP5;BP1,PP2;BS1;BS2;BP4;BP5,0.305303335189819,PP2,BS1;BP5;BP4;BS2,PS3;PM2,"PTEN c.520T>A (p.Tyr174Asn) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 10866302, PMID 29706350)PM2: Absent in large sequenced populations (PMID 27535533)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease." -NM_004333.4(BRAF):c.1595G>A,PS4;PM2;PM6;PP2;PP3,PM1;PP3;BP4,7.59744334220886,PP2;PP3,PM1;BP4,PM6;PM2,PM1;PM2;PP5,0.370512962341309,PM2,PS4;PP3;PM6;PP2,PP5;PM1,PS3;PM2;PP2,0.348472833633423,PP2;PM2,PS3,PP3;PM6;PS4,"The c.1595G>A (p.Cys532Tyr) variant in BRAF has been observed in three probands with RASopathies (PS4_Moderate; Laboratory for Molecular Medicine, Hopital Universitaire Robert Debre internal data, ClinVar SCV000197143.4) It has also been seen as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; EGL internal data, ClinVar SCV000112809.8). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Cys532Tyr variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM2, PM6, PP2, PP3." -NM_000314.6(PTEN):c.209T>C,PS3;PS4;PM2;PP2,PM1;PP3;BP4,12.6151711940765,PP2,PM1;BP4;PP3,PM2;PS4,PM1;PM2;PP3;PP5;BP1,0.378013134002686,PM2,PS3;PS4;PP2,PP5;PP3;PM1;BP1,PS4;PM2;PM6;PP2;PP3,0.304322481155395,PP2;PS4;PM2,PP3;PM6,PS3,PTEN c.209T>C (p.Leu70Pro) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 29706350)PM2: Absent in large sequenced populations (PMID 27535533).PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (internal laboratory contributor(s) ClinVar Organization ID: 26957) -NM_000314.6(PTEN):c.170T>G,PS3;PM2;PP2,,3.60957360267639,PM2,,PP2,PM1;PM2;PP3;PP5;BP1,0.366116762161255,PM2,PS3;PP2,PP5;PP3;PM1;BP1,PS3;PS4;PM2;PP2,0.315280199050903,PP2;PS3;PM2,PS4,,"PTEN c.170T>G (p.Leu57Trp) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 9256433, 29706350)PM2: Absent in large sequenced populationsPP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease." -NM_000314.6(PTEN):c.331T>C,PS3;PS4;PM2;PP2,,0.682560920715332,,,PP2;PM2,PM1;PM2;PP3;PP5;BP1,0.355661869049072,PM2,PS3;PS4;PP2,PP5;PP3;PM1;BP1,PS3;PM2;PP2,0.324536323547363,PP2;PS3;PM2,,PS4,"PTEN c.331T>C (p.Trp111Arg) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 29785012, 29706350)PM2: Absent in large sequenced populations (PMID 27535533).PS4_M: Probands with phenotype specificity score of 2-3.5. (internal laboratory contributor(s) ClinVar Organization ID: 61756, ClinVar Organization ID: 19864)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease." -NM_000314.6(PTEN):c.181C>G,PS3;PM2;PM6;PP2,,0.658978223800659,PP2,,PM2;PS3,PM1;PM2;PP3;PP5;BP1,0.35837984085083,PM2,PS3;PM6;PP2,PP5;PP3;PM1;BP1,PS3;PS4;PM2;PP2,0.320051670074463,PP2;PS3;PM2,PS4,PM6,"PTEN c.181C>G (p.His61Asp) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 29706350, PMID 17942903, PMID 21828076)PM2: Absent in large sequenced populations (PMID 27535533).PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (PMID 11748304)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease." -NM_004333.4(BRAF):c.739T>G,PS4;PM1;PM2;PP2;PP3,,0.671882152557373,PP2;PM2,,PM1;PP3,PM1;PM2;PP3;PP5,0.352654218673706,PM2;PP3;PM1,PS4;PP2,PP5,PS3;PM2;PM6;PP2,0.312778472900391,PP2;PM2,PM6;PS3,PP3;PM1;PS4,"The c.739T>G (p.Phe247Val) variant in BRAF has been identified in at least 2 independent occurrences in patients with clinical features of a RASopathy (PS4_Supporting; Partners LMM, GeneDx internal data; GTR Lab IDs 21766, 26957; ClinVar SCV000061624.5, SCV000330320.6). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). A different pathogenic missense variant (p.Phe247Leu) has been previously identified at this codon of BRAF which may indicate that this residue is critical to the function of the protein (PM5 not usable due to PM1 application; ClinVar 180784, 55793). Computational prediction tools and conservation analysis suggest that the p.Phe247Val variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM2, PM1, PP2, PP3." -NM_002834.4(PTPN11):c.167T>C,PS4;PM2;PM5;PP2;PP3,,0.59926438331604,PP2;PM2;PP3,,PM5;PS4,PM1;PM2;PP3;PP5,0.351351261138916,PM2;PP3,PP2;PS4;PM5,PP5;PM1,PS4;PM1;PM2;PP2;PP3,0.308184146881104,PP3;PP2;PS4;PM2,PM1,PM5,"The c.167T>C (p.Ile56Thr) variant in PTPN11 has been identified in 2 related patients with clinical features of a RASopathy (PS4_Supporting, PP1; Invitae internal data; GTR Lab ID 500031; ClinVar SCV000659038.1). A different pathogenic missense variant (p.Ile56Val) has been previously identified at this codon of PTPN11 which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 40485). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). The variant is located in the PTPN11 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ile56Thr variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PP1, PM2, PM5, PP2, PP3." -NM_005633.3(SOS1):c.512T>C,PS4;PM2;PM5;PM6;PP2,,0.646196365356445,PP2;PM2,,PM6;PM5,PM1;PM2;PP3;PP5,0.347958564758301,PM2,PP2;PS4;PM6;PM5,PP5;PP3;PM1,PS4;PM2;PM5;PP2;PP3,0.303659200668335,PP2;PS4;PM5;PM2,PP3,PM6,"The c.512T>C (p.Val171Ala) variant in SOS1 has been reported as an unconfirmed de novo occurrence in a patient with clinical features of a Noonan spectrum disorder (PM6; Partners LMM internal data; GTR Lab ID: 21766; ClinVar SCV000062240.5). The p.Val171Ala variant has also been identified in another independent occurrences in patients with clinical features of a familial RASopathy (PS4_Supporting; PMID: 29402968). This variant was absent from large population studies (PM2; gnomAD, http://gnomAD.broadinstitute.org). A different pathogenic missense variant (p.Val171Gly) has been previously identified at this codon of SOS1 which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 40654). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6, PM5, PM2, PS4_Supporting, PP2." -NM_000314.6(PTEN):c.737C>T,PS2;PS4;PM2;PP2,,0.816348791122437,PP2,,PM2;PS4,PM1;PM2;PP3;PP5;BP1,0.36238431930542,PM2,PS2;PS4;PP2,PP5;PP3;PM1;BP1,PS4;PM2;PM5;PM6;PP2,0.313472509384155,PP2;PS4;PM2,PM6;PM5,PS2,"PTEN c.737C>T (p.P246L) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS2_VS: At least two proven OR one proven plus two assumed de novo observations in a patient with the disease and no family history. (PMID 23934111, internal laboratory contributor(s) SCV000222227.10)PS4: Probands with phenotype specificity score of 4-15.5. (PMID 24375884, PMID 10076877, PMID 22261759, PMID 23934111, internal laboratory contributor(s) SCV000222227.10)PM2: Absent in large sequenced populations. (PMID 27535533).PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease." -NM_000314.6(PTEN):c.510T>A,PS3;PS4;PM2;PP1;PP2,,0.608964920043945,,,PP2;PM2,PM1;PM2;PP3;PP5;BP1,0.346567869186401,PM2,PP1;PS3;PS4;PP2,PP5;PP3;PM1;BP1,PS2;PS4;PM2;PP2,0.328437328338623,PP2;PS4;PM2,PS2,PP1;PS3,"PTEN c.510T>A (p.Ser170Arg) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 17942903, PMID 10866302, PMID 9256433, PMID 21828076PS4_M: Probands with phenotype specificity score of 2-3.5. (PMID 17526800, PMID 23335809, PMID 30528446)PM2: Absent in large sequenced populations (PMID 27535533)PP1: Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed. (PMID 17526800, PMID 9241266)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease." -NM_000314.6(PTEN):c.368A>G,PS3;PM1;PM2;PM6;PP2,PM1;PP3;BP4,7.65471768379211,PP2;PM1,BP4;PP3,PM6;PM2,PM1;PM2;PP3;PP5;BP1,0.388467788696289,PM2;PM1,PS3;PP2;PM6,BP1;PP3;PP5,PS3;PS4;PM2;PP1;PP2,0.304508686065674,PP2;PS3;PM2,PP1;PS4,PM1;PM6,"PTEN c.368A>G (p.His123Arg) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 29706350)PM1: Located at a residue within a catalytic motif as defined by the ClinGen PTEN Expert Panel.PM2: Absent in large sequenced populations PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (PMID 10234502)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease." -NM_005633.3(SOS1):c.322G>A,PS2;PS3;PS4;PM2;PM6;PP2,PM1,7.9345805644989,PP2;PM2,PM1,PM6;PS4,PM1;PM2;PP3;PP5,0.346650123596191,PM2,PS3;PS2;PP2;PS4;PM6,PP3;PP5;PM1,PS3;PM1;PM2;PM6;PP2,0.319913387298584,PP2;PM6;PS3;PM2,PM1,PS2;PS4,"The c.322G>A (p.Glu108Lys) variant in SOS1 has been reported as confirmed and unconfirmed occurrences in patients with clinical features of a RASopathy (PM6 and PS2; GeneDx, Partners LMM, APHP-Robert Debré Hospital internal data GTR Lab ID: 26957, 21766, 28338; ClinVar SCV000209088.9, SCV000062224.5, SCV000659144.2). The p.Glu108Lys variant has been identified in several independent occurrences in patients with clinical features of a RASopathy (PS4_Moderate; GeneDx, Partners LMM, APHP-Robert Debré Hospital internal data GTR Lab ID: 26957, 21766, 28338; ClinVar SCV000209088.9, SCV000062224.5, SCV000659144.2; PMID: 17143282; 23487764). In vitro functional studies provide some evidence that the p.Glu108Lys variant may impact protein function (PS3; PMID: 17143282, 23487764). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2, PS3, PM6, PS4_Moderate, PM2, PP2." -NM_007373.3(SHOC2):c.4A>G,PS2;PS3;PS4;PM2;PP2,,12.7059478759766,PM2,,PP2;PS3,PM1;PP5,0.373383522033691,,PM2;PS3;PS2;PP2;PS4,PP5;PM1,PS2;PS3;PS4;PM2;PM6;PP2,0.325639963150024,PS3;PP2;PM2;PS2;PS4,PM6,,"The c.4A>G (p.Ser2Gly) variant in SHOC2 has been reported as a confirmed de novo occurrence in multiple patients with clinical features of a RASopathy (PS2_VeryStrong; Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg, APHP-Robert Debré Hospital internal data; GTR ID's: 21766, 506381, 28338; ClinVar SCV000062456.5, SCV000209051.10, SCV000263045.1 PMID 19684605, 21548061, 23918763, 22528146). The p.Ser2Gly variant has been identified in at least 5 independent occurrences in patients with clinical features of a RASopathy (PS4; Institute of Human Genetics, Otto von Guericke University Magdeburg, APHP-Robert Debré Hospital internal data GTR ID's: 506381, 28338; PMID: 25563136, 24458587). In vitro functional studies provide some evidence that the p.Ser2Gly variant may impact protein function (PS3; PMID: 19684605). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the SHOC2 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PS3, PS4, PM2, PP2." -NM_002880.3(RAF1):c.775T>A,PS3;PS4;PM1;PM2;PM5;PM6;PP1;PP2;PP3,PM1;PM5,7.59474468231201,PP3;PM1;PM5;PM2,,PP2;PS3;PS4,PM1;PM2;PP3;PP5,0.350970983505249,PM2;PP3;PM1,PS3;PM5;PP2;PS4;PP1;PM6,PP5,PS2;PS3;PS4;PM2;PP2,0.361127614974976,PP2;PS4;PS3;PM2,PS2,PM6;PM5;PP3;PP1;PM1,"The c.775T>A (p.Ser259Thr) variant in RAF1 has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; APHP-Robert Debré Hospital internal data; GTR ID's: 28338). The p.Ser259Thr variant has been identified in at least 8 independent occurrences in patients with a RASopathy (PS4_Supporting; GeneDx, Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 21766, 506381 PMID: 21784453; ClinVar SCV000061360.5; SCV000209017.10). The p.Ser259Thr variant in RAF1 has been reported to segregate with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 506381; ClinVar SCV000209017.9). In vitro functional studies provide some evidence that the p.Ser259Thr variant may impact protein function (PS3; PMID: 21784453, 20052757). At least 2 other pathogenic missense variants have been previously identified at this codon of RAF1 which may indicate that this residue is critical to the function of the protein (PM5_Strong; ClinVar 40603, 40602, 228288). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of RAF1 (PM1; PMID 29493581). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ser259Thr variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6_Strong, PS4_Supporting, PP1, PM5_Strong, PM2, PM1, PP2, PP3, PS3." -NM_002880.3(RAF1):c.1082G>C,PS4;PM2;PM6;PP2;PP3,PM1;PP3;BP4,13.5859696865082,PP2;PP3,PM1;BP4,PM6;PM2,PM1;PM2;PP3;PP5,0.416451215744019,PM2;PP3,PS4;PP2;PM6,PP5;PM1,PS3;PS4;PM1;PM2;PM5;PM6;PP1;PP2;PP3,0.336107730865479,PM6;PP3;PP2;PM2;PS4,PP1;PS3;PM1;PM5,,"The c.1082G>C (p.Gly361Ala) variant in RAF1 has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 506381 ClinVar SCV000209024.9). The p.Gly361Ala variant has been identified in at least 4 independent occurrences in patients with a RASopathy (PS4_Moderate; GeneDx, Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 21766, 506381; SCV000209024.9, SCV000061333.5). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Gly361Ala variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6_Strong, PS4_Moderate, PM2, PP2, PP3." -NM_030662.3(MAP2K2):c.619G>A,PS2;PS4;PM2;PM6;PP2,,3.84742999076843,PM2,,PP2;PM6,PM1;PM2;PP5,0.393253087997437,PM2,PS4;PS2;PP2;PM6,PP5;PM1,PS4;PM2;PM6;PP2;PP3,0.326448202133179,PP2;PM6;PS4;PM2,PP3,PS2,"The c.619G>A (p.Glu207Lys) variant in MAP2K2 was absent from large population studies (PM2; gnomAD.broadinstitute.org). It has been identified in 6 individuals with clinical features of a RASopathy (PS4; SCV000204213.4, SCV000207959.10, SCV000815593.1, Otto von Guericke University Magdeburg internal data). One of these cases was a confirmed de novo occurrence and another was an unconfirmed de novo occurrence (PS2; PM6; SCV000815593.1, Otto von Guericke University Magdeburg internal data). Additionally, the c.619G>A (p.Glu207Lys) is located in MAP2K2, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4, PS2, PM6, PM2, PP2." -NM_004985.4(KRAS):c.15A>T,PS4;PM2;PM6;PP2;PP3,,0.822210550308228,PP2;PP3,,PM2;PS4,PM1;PM2;PP3;PP5,0.357481002807617,PM2;PP3,PS4;PP2;PM6,PP5;PM1,PS2;PS4;PM2;PM6;PP2,0.316963195800781,PP2;PM6;PS4;PM2,PS2,PP3,"The c.15A>T (p.Lys5Asn) variant in KRAS has been reported in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID: 17056636, GeneDx internal data). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The p.Lys5Asn variant has been identified in at least 4 independent occurrences in patients with a RASopathy (PS4_Moderate; PMID: 17056636, GeneDx, EGL Genetics internal data, ClinVar SCV000202928.7). Computational prediction tools and conservation analysis suggest that the p.Lys5Asn variant may impact protein function (PP3). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM6_Strong, PM2, PP2, PP3." -NM_000038.6(APC):c.295C>T,BS1;BS2;BP1;BP2;BP5,,0.765900611877441,BP1;BS1,,BP2;BS2,PM1;PM2;PP3;BP1,0.42238974571228,BP1,BS2;BP5;BS1;BP2,PM2;PP3;PM1,PS4;PM2;PM6;PP2;PP3,0.336857080459595,,PM6;PP3;PP2;PM2;PS4,BP2;BP5;BS2;BS1;BP1,"The c.295C>T variant in APC is a missense variant predicted to cause substitution of Arginine by Tryptophan at amino acid position 99 (p.Arg99Trp). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). The highest population minor allele frequency of the variant c.295C>T in gnomAD v2.1.1 (non-cancer) is 0.0007355 (95/129170 alleles) in the European (non-Finnish) population, which is higher than the HCCP VCEP threshold (≥ 0.001%) for BS1 (BS1). This variant has been observed in heterozygous state in more than 1000 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Invitae and Ambry Genetics internal data). It has also been observed once in a homozygous state (Ambry Genetics internal data). This variant has been observed 4 times with other APC variants deemed (likely) pathogenic by the HCCP VCEP in individuals with FAP (BP2; PMIDs 23159591, 25604157, Bonn internal data). Finally, this variant has been observed in 6 patients with an alternate molecular basis for disease (BP5; Leiden University Medical Center internal data). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS1, BS2, BP1, BP2 (VCEP specifications version 1; date of approval 12/12/2022)." -NM_000038.6(APC):c.715G>C,BS1;BS2;BP1,,0.680522441864014,BS1;BS2,,BP1,PM1;PM2;BP1,0.395238637924194,BP1,BS2;BS1,PM2;PM1,BS1;BS2;BP1;BP2;BP5,0.329262495040893,BS1;BP1;BS2,BP2;BP5,,"The c.715G>C variant in APC is a missense variant predicted to cause substitution of alanine by proline at amino acid 239 (p.Ala239Pro). This variant has been observed in ≥ 35 heterozygous individuals with no features or family history of FAP, worth ≥ 10 healthy individual points (BS2; Ambry, Invitae internal data). The highest allele frequency of this variant in gnomAD v2.1.1 (non-cancer) is 0.0002269 in East Asian population, which is higher than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) threshold (≥ 0.00001) for BS1 (BS1). Finally, APC is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS1, BS2, BP1. (VCEP specifications version 1; date of approval 12/12/2022)." -NM_000038.6(APC):c.995G>A,BS1;BS2;BP1,,0.679151058197022,BP1;BS2,,BS1,PM1;PM2;PP3;BP1,0.359575510025024,BP1,BS2;BS1,PM2;PP3;PM1,BS1;BS2;BP1,0.326711177825928,BS1;BP1;BS2,,,"The c.995G>A variant in APC is a missense variant predicted to cause substitution of Arginine by Glutamine at amino acid 332 (p.Arg332Gln). This variant has been observed in heterozygous state in >100 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics, Invitae, GeneDX internal data). The allele frequency of the c.995G>A variant in APC is 0.02% for the African sub-population (5/23604 alleles) in the non-cancer dataset from gnomAD (v2.1.1), which is higher than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) threshold (≥ 0.001%) for BS1, and therefore meets BS1. APC is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS1, BS2 and BP1 (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_000038.6(APC):c.1240C>T,BA1;BS2;BP1;BP2,PM1;PM2;PP3;BP4,7.89687919616699,BS2,PM1;BP4;PP3;PM2,;BA1,PM1;PM2;BP1;BS2,0.37108302116394,BS2;BP1,BP2;BA1,PM2;PM1,BS1;BS2;BP1,0.326195478439331,BP1;BS2,BS1,BP2;BA1,"The c.1240C>T variant in APC is a missense variant predicted to cause the substitution of arginine by cysteine at amino acid 414 (p.Arg414Cys). This variant has been observed in heterozygous state in ≥ 1000 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Invitae, Ambry, and GeneDX internal data). It has been observed in trans with a variant classified as Pathogenic by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) in an individual with FAP (BP2). The highest allele frequency of this variant is 0.001835 in European (Finnish) population, which is higher than the HCCP VCEP threshold (≥ 0.001) for BA1. Finally, APC is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BA1, BS2, BP1 and BP2 (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_000038.6(APC):c.2476T>G,BA1;BP1,PM1;PM2,12.8551404476166,BP1,PM1;PM2,BA1,PM1;PM2;BP1;BS2,0.404324531555176,BP1,BA1,BS2;PM2;PM1,BA1;BS2;BP1;BP2,0.342089176177979,BP1;BA1,BP2;BS2,,"The c.2476T>G variant in APC is a missense variant predicted to cause a substitution of leucine by valine at amino acid position 826 (p.Leu826Val). The highest population minor allele frequency in gnomAD v2.1.1 is 0.1576% in the non-cancer African/African American population, which is higher than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation threshold (>0.1%) for BA1, and therefore meets this criterion (BA1). Additionally, APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel as a gene for which primarily truncating variants are known to cause disease (BP1). Multiple lines of computational evidence suggest no splicing impact. In summary, this variant meets the criteria to be classified as Benign for FAP. ACMG/AMP criteria applied, as specified by the ClinGen/InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel: BA1, BP1 (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_000038.6(APC):c.4399C>T,BS1;BS2;BS3;BP1;BP5,PM1;PM2,13.758514881134,BP1;BS2,PM1;PM2,BS1;BP5,PM1;PM2;BP1,0.780457496643066,BP1,BS3;BP5;BS1;BS2,PM2;PM1,BA1;BP1,0.324827671051025,BP1,BA1,BS1;BP5;BS3;BS2,"The c.4399C>T variant in APC is a missense variant predicted to cause the substitution of Proline by Serine at amino acid position 1467 (p.Pro1467Ser). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in a heterozygous state in 75 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics, Invitae and GeneDX internal data). In addition, it has also been observed in 1 patient with an alternate molecular basis for disease – a pathogenic MSH6 germline variant (BP5; Melbourne Internal data). Functional study of β-catenin-regulated transcription assays indicate that this alteration suppresses CRT as effectively as the wild type (BS3_Supporting; PMID: 18199528). The highest population minor allele frequency in gnomAD v2.1.1 (non-cancer) is 0.0048% in European (non-Finnish) population, which is higher than the HCCP VCEP threshold (≥ 0.001%) for BS1, and therefore meets this criterion (BS1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS1, BS2, BS3_Supporting, BP1 and BP5 (VCEP Specification version 1, date of approval: 12/12/2022)." -NM_000038.6(APC):c.4420G>A,BA1;BS3;BP1,,3.18321204185486,BP1;BA1,,BS3,PM1;BP1;BP6;BS1;BS2,0.691692352294922,BP1,BS3;BA1,BS2;BS1;BP6;PM1,BS1;BS2;BS3;BP1;BP5,0.331009864807129,BS3;BP1,BS1;BP5;BS2,BA1,"The c.4420G>A variant in APC is a missense variant predicted to cause the substitution of Alanine by Threonine at amino acid position 1474 (p.Ala1474Thr). The highest population minor allele frequency of this variant in gnomAD v2.1.1 (non-cancer) is 1.13% in the African/African American population, which is higher than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel’s (HCCP VCEP) threshold (≥ 0.1%) for BA1, and therefore meets this criterion (BA1). Functional study of β-catenin-regulated transcription assays indicate that this alteration suppresses CRT as effectively as wild type (BS3_Supporting; PMID: 18199528). Finally, APC is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BA1, BP1, BS3_Supporting (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_000038.6(APC):c.5465T>A,BA1;BP1,,0.794879198074341,BP1,,BA1,PM1;BA1;BP1;BP6;BS1;BS2,0.420234441757202,BA1;BP1,,BS2;BS1;BP6;PM1,BA1;BS3;BP1,0.312121868133545,BP1;BA1,BS3,,"The c.5465T>A variant in APC is a missense variant predicted to cause the substitution of Valine by Asparagine at amino acid position 1822 (p.Val1822Asp). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). The highest population minor allele frequency in gnomAD v2.1.1 is 0.9598 (23897/24898 alleles) in the African/African American population, which is higher than the ClinGen APC VCEP threshold (>0.1%) for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BA1 and BP1 (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_000038.6(APC):c.7862C>G,BA1;BS2;BP1,,0.667206287384033,BP1;BS2,,BA1,PM1;BP1;BS2,0.364747047424316,BS2;BP1,BA1,PM1,BA1;BP1,0.307969331741333,BP1;BA1,,BS2,"The c.7862C>G variant in APC is a missense variant predicted to cause the substitution of Serine by Cysteine at amino acid position 2621 (p.Ser2621Cys). This variant has been observed in more than 10 heterozygous individuals over the age of 50 with no features of FAP, worth more than 10 healthy individual points (BS2; Ambry internal data). APC is defined by the ClinGen APC VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). The highest population minor allele frequency in the non-cancer cohort of gnomAD v2.1.1 is 0.5021% in the non-Finnish European population, which is higher than the ClinGen APC VCEP threshold of 0.1% for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: BA1, BS2, and BP1 (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_024675.3(PALB2):c.721A>G,BA1;BS2;BP1;BP2,,0.742187976837158,BP1;BS2,,BP2;BA1,BP1;BP4;BP6,0.376681089401245,BP1,BS2;BA1;BP2,BP6;BP4,BA1;BS2;BP1,0.300961971282959,BA1;BP1;BS2,,BP2,"The c.721A>G variant in PALB2 is a missense variant predicted to predicted to cause substitution of asparagine by aspartic acid at amino acid 241 (p.Asn241Asp). This variant has been observed in three homozygous individuals with no features of FANCN, a condition with full penetrance at an early age (Ambry Genetics). The highest population minor filtering allele frequency in gnomAD v2.1.1 is 0.005509 in the African population, which is higher than the HBOP VCEP threshold (>0.001) for BA1, and therefore meets this criterion. PALB2, in which the variant was identified, is defined by the HBOP VCEP as a gene for which primarily truncating variants are known to cause disease. In summary, this variant meets the criteria to be classified as benign for autosomal dominant hereditary breast and pancreatic cancer and autosomal recessive FANCN based on the ACMG/AMP criteria applied, as specified by the HBOP VCEP (BA1, BS2, BP1)" -NM_000038.6(APC):c.235A>G,PM2;BS2;BP1,,0.705420732498169,PM2;BS2,,BP1,PM1;PM2;BP1,0.358199596405029,BP1;PM2,BS2,PM1,BA1;BS2;BP1;BP2,0.311857223510742,BP1;BS2,BP2;BA1,PM2,"The c.235A>G variant in APC is a missense variant predicted to cause substitution of serine by glycine at amino acid 79 (p.Ser79Gly). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in 6 heterozygous individuals with no features of FAP, worth 3 healthy individual points (BS2_Supporting; Ambry Genetics Internal Data; Invitae Internal Data). In summary, this variant meets the criteria to be classified as Likely Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2_supporting, BP1. (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_000038.6(APC):c.420G>C,PM2;BS2;BP1;BP2,,0.696565866470337,BP1,,PM2;BS2,PM1;PM2;BP1,0.392112255096436,BP1;PM2,BS2;BP2,PM1,PM2;BS2;BP1,0.324557304382324,BP1;BS2;PM2,,BP2,"The c.420G>C variant in APC is a missense variant predicted to cause substitution of glutamic acid by aspartic acid at amino acid 140 (p.Glu140Asp). APCis defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in heterozygous state in 67 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics, Invitae, GeneDX internal data). This variant has also been observed in trans with a variant classified as (likely) pathogenic by the HCCP VCEP in an individual with FAP (BP2; Invitae Internal Data). Finally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as Likely Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2, BP1, BP2 (VCEP specifications version 1; date of approval 12/12/2022)." -NM_000038.6(APC):c.1487C>T,PM2;BS2;BP1,,0.791619539260864,BP1;PM2,,BS2,PM1;PM2;PP3;BP1,0.397652149200439,BP1;PM2,BS2,PP3;PM1,PM2;BS2;BP1;BP2,0.309634447097778,BP1;BS2;PM2,BP2,,"The c.1487C>T variant in APC is a missense variant predicted to cause substitution of threonine by isoleucine at amino acid 496 (p.Thr496Ile). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in a heterozygous state in 18 unrelated healthy adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics, Invitae, and GeneDX internal data). In summary, this variant meets the criteria to be classified as Likely Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2 and BP1 (VCEP specifications version 1.0, date of approval: 12/12/2022)." -NM_000038.6(APC):c.4906G>T,PM2;BS2;BP1;BP2,PM1,8.05782437324524,PM2,PM1,BP1;BS2,PM1;PM2;PP3;BP1,0.36128044128418,BP1;PM2,BP2;BS2,PP3;PM1,PM2;BS2;BP1,0.346704483032226,BP1;BS2;PM2,,BP2,"The c.4906G>T variant in APC is a missense variant predicted to cause the substitution of aspartate by tyrosine at amino acid position 1636 (p.Asp1636Tyr). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in trans with the variant c.3100G>T (p.Glu1034*) (Bonn internal data) which is classified as Pathogenic by the HCCP VCEP in an individual with FAP (BP2). This variant has been observed in heterozygous state in 11 unrelated healthy adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics internal data). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, although there are both pathogenic and benign types of evidence for this variant, the pathogenic/benign evidence is not considered inconsistent with the final Likely Benign classification for FAP. ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2, BP1, and BP2 (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_000038.6(APC):c.8438C>A,PM2;BS2;BP1,PM1;BP7,9.49743723869324,BP1;PM2,PM1;BP7,BS2,PM1;PM2;BP1,0.388001680374146,BP1;PM2,BS2,PM1,PM2;BS2;BP1;BP2,0.315003395080566,BP1;BS2;PM2,BP2,,"The c.8438C>A variant in APC is a missense variant predicted to cause the substitution of Threonine by Lysine at amino acid position 2813 (p.Thr2813Lys). This variant has been observed in ≥ 3 individuals with no features or family history of FAP, which is worth 3 healthy individual points (BS2_supporting; Invitae and Ambry internal data). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant is absent from gnomAD v2.1.1 (PM2_supporting). In summary, this variant meets the criteria to be classified as Likely Benign for FAP. Although there are both pathogenic and benign types of evidence for this variant, the pathogenic evidence is not considered inconsistent with the final classification. ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2_supporting, and BP1. (VCEP specifications version 1; date of approval: 12/12/2022)." -NM_000277.2(PAH):c.472C>T,PS3;PM2;PM3;PP3;PP4,PM1;PM2;PM5;PP3;BP4,7.82847857475281,PM2;PP3,PM1;PM5;BP4,PP4,PM1;PM2;PP5;BP1,0.374401569366455,PM2,PM3;PP3;PP4;PS3,PP5;BP1;PM1,PM2;BS2;BP1,0.340309619903564,PM2,BP1;BS2,PP3;PM3;PP4;PS3,"PAH-specific ACMG/AMP criteria applied: PM2: Extremely low frequency. ExAC MAF=0.00019.; PP3: Predicted deleterious in SIFT, Polyphen-2, MutationTaster. REVEL=0.939; PS3: 2% mutant enzyme activity in BioPKU; PP4_Moderate: Detected in at least 3 patients with PAH deficiency. BH4 deficiency ruled out in 1 patient. (PMID:1307609; PMID:10429004; PMID:9634518); PM3_Strong: Detected with 3 pathogenic/likely pathogenic variants (PMID:14681498; PMID:23430918). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PP3, PS3, PP4_Moderate, PM3_Strong)." -NM_000277.2(PAH):c.533A>G,PS3;PM2;PM3;PP3;PP4,PM1;PM2,7.92781496047974,PM2,PM1,PS3;PP3,PM1;PM2;PP3;PP5;BP1,0.379242897033691,PP3;PM2,PM3;PP4;PS3,PP5;BP1;PM1,PS3;PM2;PM3;PP3;PP4,0.284643173217773,PM3;PP3;PS3;PM2;PP4,,,"PAH-specific ACMG/AMP criteria applied: PM2: Absent from 1000G, ESP. ExAC MAF=0.00017; PP3: Deleterious effect predicted in SIFT, Polyphen2, MutationTaster. REVEL=0.841; PS3: 39% residual phenylalanine hydroxylase activity (PMID:17935162); PP4_Moderate: Detected in 6 PKU patients. BH4 deficiency excluded. Upgraded per ClinGen PAHEP. (PMID:18294361; PMID:9634518); PM3_Strong: In trans with 3 pathogenic variants (PMID:18294361). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PP3, PS3, PP4_Moderate, PM3_Strong)." -NM_000277.2(PAH):c.194T>C,PS3;PM3;PP3;PP4,PM1;PM2;PM5;PP3;BP4,7.47418713569641,PP3,PM1;PM5;BP4;PM2,PP4,PM1;PM2;PP3;PP5;BP1,0.358322143554687,PP3,PM3;PP4;PS3,PP5;BP1;PM1;PM2,PS3;PM2;PM3;PP3;PP4,0.296109437942505,PP3;PM3;PS3;PP4,PM2,,"PAH-specific ACMG/AMP criteria applied: PM3_VeryStrong: Detected with Y414C (P), R408W (P), P281L (P), IVS10nt-11 (P), R252W (P/LP), and R243Q(P). (PMID:12501224; PMID:1301201; PMID:10767174); PP3: Predicted dleterious in SIZFT, Polyphen2, MutationTaster. REVEL=0.985; PP4_Moderate: Detected in a patient with mild PKU. BH4 deficiency excluded. Upgraded per ClinGen PAH EP. (PMID:12501224); PS3: 25% mutant enzyme activity in COS cells as compared in wt (PMID:1301201). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM3_VeryStrong, PP3, PP4_Moderate, PS3)." -NM_004999.3(MYO6):c.1025C>T,PP3;BA1,PM2;BP7,4.69298410415649,BA1,PM2;BP7,,PM2;PP3;BP6;BS2,0.382071018218994,PP3,BA1,BS2;BP6;PM2,PM1;PM2;PM5;PP3;PP5,0.308812379837036,PP3,PM1;PM5;PP5;PM2,BA1,"The filtering allele frequency of the p.Ala342Val variant in the MYO6 gene is 0.21% for European (non-Finnish) chromosomes by gnomAD (304/129090 with 95% CI), and one homozygous European (Finnish) individual, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal dominant hearing loss variants (BA1). The REVEL computational prediction analysis tool produced a score of 0.905, however, this information is not predictive of pathogenicity on its own and is not considered in conflict with evidence that supports a benign interpretation. In summary, the HL EP classified this variant as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1." -NM_000441.1(SLC26A4):c.1069G>A,PP3;BA1,PM1;PM2,14.513293504715,BA1,PM1;PM2,,PM1;PP3;BP1;BP6;BS2,1.34810471534729,PP3,BA1,BS2;BP1;BP6;PM1,PP3;BA1,0.313730001449585,PP3;BA1,,,"The filtering allele frequency of the p.Ala357Thr variant in the SLC26A4 gene is 0.47% for African chromosomes by gnomAD (136/24968 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive Pendred syndrome variants (BA1). The REVEL computational prediction analysis tool produces a score of 0.849, which is above the threshold necessary to apply PP3; however, this information is not predictive of pathogenicity on its own and is not considered in conflict with evidence that supports a benign interpretation. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1." -NM_000527.5(LDLR):c.970G>A,PP1;PP3;BA1;BS2;BP2,,3.14010524749756,PP3;BA1;BS2,,PP1;BP2,PM1;PP2;PP3;BP1;BS1;BS2,0.426384925842285,PP3;BS2,BP2;PP1;BA1,PP2;BP1;PM1;BS1,PP3;BA1,0.330469131469726,PP3;BA1,,PP1;BP2;BS2,"The NM_000527.5(LDLR):c.970G>A (p.Gly324Ser) variant is classified as Benign for Familial Hypercholesterolemia by applying evidence codes (BA1, BS2, BP2, PP1 and PP3) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: BA1 - FAF = 0.01153 (1.153%) in African/African American exomes (gnomAD v2.1.1). BS2 - Identified in 4 heterozygous non-affected family members from different labs.BP2 - variant identified 1 index case with heterozygous FH phenotype who is double heterozygous with NM_000384.3(APOB):c.10580G>A p.Arg3527Gln (ClinVar ID 17890) - classified as Pathogenic by the general ACMG guidelines (Chora et al., 2018).PP1 - variant segregates with phenotype in 2 informative meiosis in 1 family from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge.PP3 - REVEL = 0.815.Variant has 1 stand alone, 1 Strong and 1 Supporting evidence codes towards Benign, enough to classify as Benign, and only 2 Supporting codes towards Pathogenic. The Benign criteria overwhelms the Pathogenic criteria, so we are confident in classifying this variant as Benign." -NM_000441.1(SLC26A4):c.1363A>T,PP3;BA1,,0.686535835266113,PP3,,BA1,PM1;PP3;BP1;BP6;BS2,0.345483303070068,PP3,BA1,BS2;BP1;BP6;PM1,PP1;PP3;BA1;BS2;BP2,0.292094707489014,PP3;BA1,PP1;BP2;BS2,,"The filtering allele frequency of the p.Ile455Phe variant in the SLC26A4 gene is 3% (981/30778) of South Asian chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which is a high frequency that is consistent with benign classification based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1)." -NM_000545.8(HNF1A):c.1135C>G,PP3;BA1,,0.668957233428955,BA1,,,PM1;PM2;PP3,0.360151767730713,PP3,BA1,PM1;PM2,PP3;BA1,0.322887182235718,PP3;BA1,,,"The c.1135C>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of proline to alanine at codon 379 (p.(Pro379Ala)) of NM_000545.8. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.9639, which is greater than the MDEP VCEP threshold of 0.70 (PP3). While this variant has been identified in >20 unrelated individuals with diabetes in the literature (ClinVar ID 431970, PMID:18003757, PMID: 23348805, PMID: 29207974, PMID: 21761282, PMID: 23607861), it has a Popmax Filtering allele frequency in gnomAD 2.1.1 of 0.0005091, which is greater than the MDEP threshold for BA1 (greater than 0.0001) (BA1). Therefore, PS4 cannot be applied. While another variant at this codon, c.1136C>G (p.(Pro379Arg)), is classified as Pathogenic by the MDEP, the c.1135C>G meets the criteria to be classified as benign for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.1.1, approved 8/11/2023): BA1, PP3. It may, however, confer an increased risk of type 2 diabetes (OR = 11.8, p = 0.0007324 at type2diabetesgenetics.org)." -NM_000545.8(HNF1A):c.1136C>A,PM5;PP3;PP4;BA1,PM1;PM2;PM5;PP3;BP4,289.539047002792,PM5;PP3,PM1;BP4;PM2,BA1,PM1;PM2;PP3,0.405366659164429,PP3,PP4;PM5;BA1,PM1;PM2,PP3;BA1,0.37108302116394,PP3;BA1,,PM5;PP4,"The c.1136C>A variant in the HNF1 homeobox A gene, HNF1A causes an amino acid change of proline to histidine at codon 379 (p.(Pro379His)) of NM_000545.8. This variant has a Popmax Filtering allele frequency in gnomAD 2.1.1 of 0.0001567, which is greater than the MDEP threshold for BA1 (0.0001)(BA1). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.969, which is greater than the MDEP VCEP threshold of 0.70 (PP3). Functional studies demonstrated the p.Pro379His protein has transcriptional activity on insulin promoter 62% of WT in RINm5f cells and 78% of WT in HeLA cells (PMID 15883474). While one cell line is greater than the MDEP BS3 cutoff of 75%, one is between the ClinGen MDEP cutoffs for PS3 (<=40%) and BS3, and therefore neither PS3 nor BS3 is applied. This variant was identified in one family and segregated with diabetes with two informative meioses; however, this does not meet the thresholds for PP1 or PS4 set by the ClinGen MDEP (PMIDs: 27236918, 15883474). An individual in this family had a clinical history highly specific for HNF1A-monogenic diabetes (MODY probability calculator result >50%, negative genetic testing for HNF4A, and antibody negative) (PP4_Moderate; PMID 15883474). Another missense variant, c.1136C>G (p.Pro379Arg), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Pro379His (PM5_Supporting). In summary, c.1136C>A meets the criteria to be classified as benign for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.1.0, approved 8/11/2023): BA1, PM5_Supporting, PP4_Moderate, PP3." -NM_001110792.2(MECP2):c.968C>T,PP3;BS1;BS2;BP5,PM1;PM2,7.84452056884766,BS2,PM1;PM2,PP3;BS1,PM1;PM2;PP3;BP1,0.363806486129761,PP3,BS2;BP5;BS1,PM1;BP1;PM2,PM5;PP3;PP4;BA1,0.296879529953003,PP3,PM5;PP4;BA1,BS1;BP5;BS2,"The allele frequency of the p.Thr311Met variant in MECP2 (NM_004992.3) is 0.022% and 0.01% in ""Other"" and South Asian sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Thr311Met variant is observed in at least 2 unaffected individuals (GeneDx internal database) (BS2) and found in 2 patients with an alternate molecular basis of disease (Baylor Genetics internal database, Invitae internal database) (BP5). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own (PP3). As this variant meets 2 strong and 1 supporting benign criteria it can be classified as benign even though in silico predictions meet PP3. In summary, the p.Thr311Met variant in MECP2 is classified as benign for Rett syndrome based on the ACMG/AMP criteria (BS1, BS2, BP5)." -NM_004985.4(KRAS):c.15A>T,PS4;PM2;PM6;PP2;PP3,PS1;PP3;BP4,15.3030745983124,PM2;PP3,PS1;BP4,PP2;PM6,PM1;PM2;PP3;PP5,0.365798234939575,PP3;PM2,PM6;PS4;PP2,PM1;PP5,PP3;BS1;BS2;BP5,0.289863109588623,PP3,BS1;BP5;BS2,PP2;PM6;PS4;PM2,"The c.15A>T (p.Lys5Asn) variant in KRAS has been reported in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID: 17056636, GeneDx internal data). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The p.Lys5Asn variant has been identified in at least 4 independent occurrences in patients with a RASopathy (PS4_Moderate; PMID: 17056636, GeneDx, EGL Genetics internal data, ClinVar SCV000202928.7). Computational prediction tools and conservation analysis suggest that the p.Lys5Asn variant may impact protein function (PP3). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM6_Strong, PM2, PP2, PP3." -NM_004333.4(BRAF):c.1785T>G,PS4;PM1;PM2;PM6;PP2;PP3,PS1;PM1;PP3;BP4,12.6560122966766,PP2;PM1;PP3,PS1;BP4,PM2;PS4,PM1;PM2;PP5,0.367579221725464,PM1;PM2,PM6;PS4;PP3;PP2,PP5,PS4;PM2;PM6;PP2;PP3,0.336376667022705,PM6;PP3;PP2;PM2;PS4,,PM1,"The c.1785T>G (p.Phe595Leu) variant in BRAF has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID 19206169, 18042262; GTR ID's: 26957, 21766; ClinVar SCV000203922.4, SCV000207755.12). The variant has also been identified in at least 2 independent occurences in patients with clinical features of a RASopathy (PS4_Supporting; APHP-Robert Debré internal data; GTR ID 28338). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581, 16439621). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Phe595Leu variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PM6_Strong, PM2, PM1, PP2, PP3, PS4_Supporting." -NM_004985.4(KRAS):c.101C>T,PS2;PM2;PM5;PP2;PP3,,4.86893200874329,PP2;PM2;PM5,,PS2;PP3,PM1;PM2;PP3;PP5,0.38914942741394,PP3;PM2,PP2;PS2;PM5,PM1;PP5,PS4;PM1;PM2;PM6;PP2;PP3,0.302638530731201,PP3;PP2;PM2,PM1;PM6;PS4,PS2;PM5,"The c.101C>T (p.Pro34Leu) variant in KRAS has been reported as a confirmed de novo occurrence in a patient with clinical features of a RASopathy (PS2; PMID 17056636, 20949621). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). A different pathogenic missense variant has been previously identified at this codon of KRAS which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 12590). Computational prediction tools and conservation analysis suggest that the p.Pro34Leu variant may impact the protein (PP3; PMID: 24803665). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PS2, PM2, PM5, PP3, PP2." -NM_004985.4(KRAS):c.173C>T,PS3;PM1;PM2;PM6;PP2;PP3,,0.658904314041138,PP2;PM2;PP3,,PM1;PM6,PM1;PM2;PP3;PP5,0.357168197631836,PM1;PP3;PM2,PS3;PP2;PM6,PP5,PS2;PM2;PM5;PP2;PP3,0.306113719940185,PP3;PP2;PM2,PS2;PM5,PM1;PM6;PS3,"The c.173C>T (p.Thr58Ile) variant in KRAS has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6_Strong; PMID 23321623, 20112233, 16921267, 16474405, 22488832, 18247425, 20949621). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). In vitro functional studies provide some evidence that the p.Thr58Ile variant may impact protein function (PS3; PMID: 23321623, 20949621, 16921267). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of KRAS (PM1; PMID 29493581). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Thr58Ile variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6_Strong, PS3, PM2, PM1, PP2, PP3." -NM_176795.4(HRAS):c.173C>T,PS1;PS4;PM1;PM2;PM6;PP2;PP3,,0.674533367156982,PP2;PP3;PS1,,PM1;PS4;PM2,PM1;PM2;PP3;PP5,0.37951135635376,PM1;PP3;PM2,PM6;PS4;PS1;PP2,PP5,PS3;PM1;PM2;PM6;PP2;PP3,0.538906812667847,PM6;PP3;PP2;PM2;PM1,PS3,PS4;PS1,"The c.173C>T (p.Thr58Ile) variant in HRAS has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; PMID 20112233, 16474405). Also, at least 2 independent occurrences of this variant have been detected in patients with a RASopathy (PS4_Supporting; PMID: 22488832, 18247425, 23321623, 20949621, 16921267). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The p.Thr58Ile variant in HRAS is analogous to the same previously established amino acid change in the KRAS gene and the ClinGen RASopathy Expert Panel has defined that the pathogenicities of analogous variants in the HRAS and KRAS genes are correlated based on the assumption that a known functional residue in one gene is equivalent to other functions within that subgroup (PS1; 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of HRAS (PM1; PMID 29493581). The variant is in HRAS, which has been defined by the ClinGen RASopathy Expert Panel as a gene with low rate of benign missense with missense variants commonly being pathogenic (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Thr58Ile variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6, PS4_Supporting, PM2, PS1, PM1, PP2, PP3." -NM_005343.3(HRAS):c.350A>G,PS3;PM1;PM2;PM6;PP3,,0.758193969726563,PM1;PP3,,PM6;PM2,PM1;PM2;PP3;PP5,0.36811375617981,PM1;PP3;PM2,PS3;PM6,PP5,PM1;PM2;PP3;PP5,0.311939001083374,PP3;PM1;PM2,PP5,PM6;PS3,"The c.350A>G (p.Lys117Arg) variant in HRAS has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID 16443854, 16155195). In vitro functional studies provide some evidence that the p.Lys117Arg variant may impact protein function (PS3; PMID 17979197, 21850009). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of HRAS (PM1; PMID 29493581). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Computational prediction tools and conservation analysis suggest that the p.Lys117Arg variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PM6_Strong, PS3, PM1, PM2, PP3." -NM_005633.3(SOS1):c.1642A>C,PS2;PS3;PM1;PM2;PP2;PP3,,0.665717363357544,PP2;PM1;PM2,,PS2;PP3,PM1;PM2;PP3;PP5,0.362068653106689,PM1;PP3;PM2,PS3;PS2;PP2,PP5,PM1;PM2;PP3;PP5,0.320886850357056,PP3;PM1;PM2,PP5,PP2;PS2;PS3,"The c.1642A>C (p.Ser548Arg) variant in SOS1 has been reported as a confirmed de novo occurrence in a patient with clinical features of a RASopathy (PS2_VeryStrong; PMID 17143282). In vitro functional studies provide some evidence that the p.Ser548Arg variant may impact protein function (PS3; PMID 23487764). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of SOS1 (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Ser548Arg variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID: 29493581): PP2, PP3, PM1, PM2, PS3 PS2_VeryStrong." -NM_005633.3(SOS1):c.806T>C,PS2;PM1;PM2;PP2;PP3,,0.658915042877197,PP2;PM1;PM2,,PS2;PP3,PM1;PM2;PP3;PP5,0.45712423324585,PM1;PP3;PM2,PP2;PS2,PP5,PS2;PS3;PM1;PM2;PP2;PP3,0.381702899932861,PP3;PP2;PM2;PS2;PM1,PS3,,"The c.806T>C (p.Met269Thr) variant in SOS1 has been reported in the literature in at least 2 unconfirmed and 1 confirmed de novo occurrences in patients with clinical features of a RASopathy (PS2_VeryStrong; PMID 17586837; 19953625, 20683980). It has also been reported as a confirmed de novo occurrence in a patient with clinical features of a RASoapthy (PMID: 20683980). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is in SOS1, which has been defined by the ClinGen RASopathy Expert Panel as a gene with low rate of benign missense with missense variants commonly being pathogenic (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Met269Thr variant may impact the protein (PP3). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of SOS1 (PM1; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID: 29493581): PP2, PP3, PM1, PM2, PS2_VeryStrong." -NM_002880.3(RAF1):c.1472C>T,PS3;PM1;PM2;PP2;PP3,PM1;PM5;PP3;BP4,8.11765480041504,PP2;PM1;PP3;PM2,PM5;BP4,PS3,PM1;PM2;PP3;PP5,0.383171319961548,PM1;PM2;PP3,PP2;PS3,PP5,PS2;PM1;PM2;PP2;PP3,0.313710212707519,PP3;PM1;PP2;PM2,PS2,PS3,"The c.1472C>T (p.Thr491Ile) variant in RAF1 has been reported in the literature in at least one individual with clinical features of a RASopathy (PS4 not met; PMID 17603483). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Thr491Ile variant may impact the protein (PP3). In vitro functional studies provide some evidence that the p.Thr491Ile variant may impact protein function (PS3; 20679480). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of RAF1 (PM1; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PP2, PP3, PM1, PM2, PS3." -NM_002755.3(MAP2K1):c.389A>G,PS2;PS3;PM1;PM2;PP2;PP3,PM1;PP3;BP4,7.968829870224,PP2;PM1;PP3,BP4,PM2;PS2,PM1;PM2;PP2;PP3;PP5,0.403749942779541,PM1;PM2;PP2;PP3,PS2;PS3,PP5,PS3;PM1;PM2;PP2;PP3,0.296164512634277,PP3;PS3;PP2;PM2;PM1,,PS2,"The c.389A>G (p.Tyr130Cys) variant in MAP2K1 has been reported as a confirmed de novo occurrence in at least 2 patients with clinical features of a RASopathy (PS2_VeryStong; PMID 16439621, 17551924, 18042262). In vitro functional studies provide some evidence that the p.Tyr130Cys variant may impact protein function (PS3; PMID 18413255, 23093928, 17981815). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the MAP2K1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K1 (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Tyr130Cys variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PP3, PS3, PM2, PP2, PM1." -NM_002755.3(MAP2K1):c.275T>G,PS2;PS4;PM2;PP2;PP3,PM1,7.97276663780212,PP2,PM1,PM2;PP3,PM1;PM2;PP2;PP3;PP5,0.395981073379517,PM2;PP2;PP3,PS2;PS4,PM1;PP5,PS2;PS3;PM1;PM2;PP2;PP3,0.30141806602478,PP3;PP2;PS2;PM2,PM1;PS3,PS4,"The c.275T>G (p.Leu92Arg) variant in MAP2K1 has been reported in at least 3 de novo occurrences, including 1 case with parental confirmation, in patients diagnosed with a RASopathy (PS2_VeryStrong, PS4_Moderate; GeneDx, APHP-Robert Debre hospital, Laboratory for Molecular Medicine internal data; ClinVar SCV000207940.11, SCV000965969.1, SCV000061251.5). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The variant is located in the MAP2K1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Leu92Arg variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PS4_Moderate, PM2, PP2, PP3." -NM_000277.2(PAH):c.529G>A,PM2;PM3;PM5;PP3;PP4,PM1;PM2;PM5,8.22266864776611,PM5;PM2,PM1,PP3,PM1;PM2;PP3;PP5;BP1,0.469707727432251,PM2;PP3,PM3;PM5;PP4,PM1;BP1;PP5,PS2;PS4;PM2;PP2;PP3,0.281403064727783,PP3;PM2,PP2;PS2;PS4,PM3;PP4;PM5,"The c.529G>A (p.Val177Met) variant in PAH was detected in a patient with Mild hyperphenylalaninemia (BH4 deficiency ruled out). PMID: 12501224 It has been detected with known pathogenic variants R408W (PMID: 12501224), and IVS12+1G>A (PMID: 23764561). It is absent from 1000G, ESP, and gnomAD; and at extremely low frequency in ExAC (MAF=0.00003). A deleterious effect is predicted in SIFT, Polyphen-2, MutationTaster, and REVEL=0.89. A different pathogenic missense change has been seen at this amino acid (V177L). In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM3_strong, PM2, PM5, PP4_Moderate, PP3." -NM_000277.2(PAH):c.848T>A,PM2;PM3;PM5;PP3;PP4,PM1,8.48596286773682,PM5;PP3,PM1,PM2;PM3,PM1;PM2;PP3;PP5;BP1,0.480615854263306,PM2;PP3,PM3;PM5;PP4,PM1;BP1;PP5,PM2;PM3;PM5;PP3;PP4,0.317513227462768,PM3;PM5;PP3;PM2;PP4,,,"The c.848T>A (p.Ile283Asn) variant in PAH is absent from population databases and predicted damaging with in silico predictors. It is a novel missense change in a residue where a different pathogenic variant has been identified (c.847A>T (p.Ile283Phe). It has been identified in multiple affected individuals in trans with known pathogenic variants (PMID: 9521426, 26413448), and was identified in a patient in which a defect in BH4 metabolism had been excluded. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM3_strong, PM2, PM5, PP4_Moderate, PP3." -NM_000277.2(PAH):c.799C>G,PS3;PM2;PM3;PP3;PP4,PM1;PP3;BP4,14.820294380188,PP3,PM1;BP4,PM2;PP4,PM1;PM2;PP3;PP5;BP1,0.417472362518311,PM2;PP3,PM3;PS3;PP4,PM1;BP1;PP5,PM2;PM3;PM5;PP3;PP4,0.302389144897461,PP3;PM3;PP4;PM2,PM5,PS3,"The c.799C>G (p.Gln267Glu) variant in PAH was reported in 2 Chinese PKU patients. BH4 deficiencies not completely ruled out. (PMID: 26600521) This variant was detected with known pathogenic variants p.R111X (PMID: 16256386), and D101N (not in ClinVar, PMID: 26600521). It is absent from ExAC, gnomAD, 1000G, and ESP. This variant is predicted deleterious in SIFT, Polyphen2, MutationTaster, and REVEL=0.935. This variant was expressed in e. coli using a rat Q267E mutant. It has 11% activity of wt. based on duplicate determinations of a single clone. (PMID: 7914195). In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM2, PM3, PS3, PP3, PP4." -NM_004086.2(COCH):c.151C>T,PS4;PM2;PP1;PP3,,3.88356995582581,PM2,,PS4;PP3,PM1;PM2;PP2;PP3;PP5,0.443260192871094,PM2;PP3,PP1;PS4,PM1;PP2;PP5,PS3;PM2;PM3;PP3;PP4,0.314664840698242,PP3;PM2,PM3;PP4;PS3,PP1;PS4,"The c.151C>T (p.Pro51Ser) variant in COCH has been reported to segregate with late onset progressive hearing loss and vestibular dysfunction in > 25 family members (PP1_S; PMID: 9931344, 11332404). The variant meets PM2 and has been observed in at least 15 affected probands (PS4, PMID: 28733840, 16151338, 11332404). The allele frequency of the p.Pro51Ser variant is 0.001% (1/111716) of European chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org), which is a low enough frequency to award PM2 based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal dominant hearing loss (PM2). Computational prediction tools and conservation analysis suggest that the p.Pro51Ser variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hearing loss based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PP1_S, PS4, PM2, PP3." -NM_000277.2(PAH):c.1278T>C,BA1;BP4,,0.85227108001709,BP4,,BA1,BP4;BP6;BP7;BS1,0.39901065826416,BP4,BA1,BP6;BP7;BS1,PS4;PM2;PP1;PP3,0.304616212844849,,PP3;PP1;PS4;PM2,BP4;BA1,"PAH-specific ACMG/AMP criteria applied: BA1: MAF=0.16641; BP4: no impact on gene in SIFT, Polyphen2, MutationTaster. In summary this variant meets criteria to be classified as benign for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (BA1, BP4)." -NM_000277.2(PAH):c.707-7A>T,BA1;BP4,PVS1,0.943348407745361,BP4,PVS1,BA1,,0,,,,BA1;BP4,0.318448066711426,BP4;BA1,,,"PAH-specific ACMG/AMP criteria applied: BA1: Highest MAF=0.10514 in 1000G. 35 homozygotes in ExAC; BP4: HSF: No significant splicing motif alteration detected. This mutation has probably no impact on splicing. CADD=1.163344. In summary this variant meets criteria to be classified as benign for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (BA1, BP4)." -NM_000277.2(PAH):c.735G>A,BA1;BS2;BP4,,0.67733359336853,BA1;BP4,,,BA1;BP4;BP7;BS1,0.365957736968994,BA1;BP4,BS2,BS1;BP7,BA1;BP4,0.315269947052002,BP4;BA1,,BS2,"The c.735G>A (p.Val245=) variant in PAH has a MAF of 0.29058 in ExAC (BA1; http://exac.broadinstitute.org) with 6,524 homozygotes (BS2). This is a synonymous variant, predicted tolerated and benign in SIFT, Polyphen. MutationTaster predicted polymorphism with no abrogation of splice sites (BP4). In summary, this variant meets criteria to be classified as benign." -NM_005633.3(SOS1):c.1230G>A,BA1;BP4;BP5;BP7,PM2;BP7,2.09849143028259,BP7;BP4,PM2,BA1,BP4;BP6;BP7;BS1;BS2,0.392003297805786,BP4;BP7,BP5;BA1,BS2;BS1;BP6,BA1;BS2;BP4,0.311575174331665,BP4;BA1,BS2,BP5;BP7,"The c.1230G>A (p.Gln410=) variant in SOS1 has been identified in a patient with an alternate molecular basis for disease (BP5; Partners LMM internal data GTR Lab ID: 21766 ClinVar SCV000062189.5). This variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Computational prediction tools and conservation analysis suggest that the p.Gln410= variant does not impact the protein (BP4). The filtering allele frequency of the c.1230G>A (p.Gln410=) variant in the SOS1 gene is 4.69% for Latino chromosomes by the Exome Aggregation Consortium (580/11526 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP5, BP7, BP4." -NM_007373.3(SHOC2):c.1302C>T,BA1;BP4;BP5;BP7,PM2,2.26057815551758,BP4,PM2,BP7;BA1,BP4;BP6;BP7,0.50866961479187,BP4;BP7,BP5;BA1,BP6,BA1;BP4;BP5;BP7,0.321614265441894,BP4;BP5;BP7;BA1,,,"The c.1302C>T (p.Asn434=) variant in the SHOC2 gene has been identified in a patient with an alternate molecular basis for disease (BP5; ClinVar SCV000171633.12). The silent p.Asn434= variant is not predicted by MaxEntScan to impact splicing (BP7, BP4).The filtering allele frequency of the c.1302C>T (p.Asn434=) variant is 0.74% for African chromosomes by the Exome Aggregation Consortium (87/9772 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP5, BP4, BP7." -NM_002834.4(PTPN11):c.1658C>T,BA1;BP4,PM2;BP7,8.43284821510315,BA1,PM2;BP7,,PM1;PM2;BP6;BS2,0.362895965576172,,BP4;BA1,PM2;BS2;PM1;BP6,BA1;BP4;BP5;BP7,0.296144723892212,BP4;BA1,BP5;BP7,,"The filtering allele frequency of the c.1658C>T (p.Thr553Met) variant in the PTPN11 gene is 0.048% for European (Non-Finnish) chromosomes by the Exome Aggregation Consortium (49/66556 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). Computational prediction tools and conservation analysis suggest that the p.Thr553Met variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP4." -NM_004333.4(BRAF):c.1227A>G,BA1;BP4;BP5;BP7,PM2,1.99128532409668,BP7;BP4,PM2,BA1;BP5,BP4;BP6;BP7;BS1;BS2,0.41414737701416,BP4;BP7,BP5;BA1,BS2;BS1;BP6,BA1;BP4,0.30139946937561,BP4;BA1,,BP5;BP7,"The filtering allele frequency of the c.1227A>G (p.Ser409=) variant in the BRAF gene is 0.313% for European (Non-Finnish) chromosomes by the Exome Aggregation Consortium (233/66620 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). Additionally, this variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). The p.Ser409= variant has been identified in a patient with an alternate molecular basis for disease (BP5; GeneDx, Partners LMM, EGL Genetics internal data; GTR ID's: 21766, 26957, 500060; SCV000057203.8; SCV000061570.5; SCV000112807.7). Computational prediction tools and conservation analysis suggest that the p.Ser409= variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied: BA1, BP7, BP5, BP4." -NM_001754.4(RUNX1):c.614-34C>T,BA1;BP2;BP4,BP7,2.41879773139954,BP4,BP7,BA1,,0,,,,BA1;BP2;BP4,0.300057888031006,BP2;BP4;BA1,,,"The NM_001754.4:c.614-34C>T variant has a MAF of 1 (100%) in gnomAD cohort that is ≥ 0.0015 (0.15%) (BA1). This variant is detected in homozygous state in gnomAD population database (BP2). This intronic variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created (BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4." -NM_000441.2(SLC26A4):c.416-7T>C,BA1;BP4;BP7,PM1;PM2;BP7,1.94276523590088,BP7;BA1,PM1;PM2,,,0,,,,BA1;BP4;BP7,0.325613260269165,BP4;BP7;BA1,,,"The filtering allele frequency of the c.416-7T>C variant in SLC29A4 is 0.59% (169/24960) in African chromosomes in gnomAD (BA1). Additionally, computational prediction tools and conservation analysis suggest that the c.416-7T>C variant may not impact the protein (BP4, BP7). In summary, this variant meets criteria to be classified as benign for autosomal recessive Pendred syndrome. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP7, BP4." -NM_005633.3(SOS1):c.*4C>T,BA1;BP4;BP7,PM2;BP7,5.61773633956909,BP7;BA1,PM2,,,0,,,,BA1;BP4;BP7,0.299153566360474,BP4;BP7;BA1,,,"The c.*4C>T variant in SOS1 is classified as benign because it has been identified in 0.05383% (95% CI of 27/35402) of Latino alleles in gnomAD (BA1; https://gnomad.broadinstitute.org). It does not alter an amino acid residue, is not located within the splice consensus site, and computational splice prediction tools do not predict an impact on splicing (BP4, BP7). ACMG/AMP Criteria applied: BA1, BP4, BP7." -NM_004985.5(KRAS):c.-160A>G,BA1;BP4;BP7,BP7,1.81799578666687,BP7;BP4,,BA1,,0,,,,BA1;BP4;BP7,0.30588436126709,BP4;BP7;BA1,,,"The c.-160A>G variant in KRAS is classified as benign because it has been identified in 0.22088% (95% CI of 27/8628) of African alleles in gnomAD (BA1; https://gnomad.broadinstitute.org). This variant is not located within the splice consensus sequence and computational splice site prediction tools do not predict an impact on splicing (BP4, BP7). ACMG/AMP Criteria applied: BA1, BP4, BP7." -NM_001754.4(RUNX1):c.1086G>C,BA1;BP4;BP7,PM2;BP7,1.88257908821106,BP7;BP4,PM2,BA1,BP4;BP6;BP7;BS2,0.373845815658569,BP7;BP4,BA1,BS2;BP6,BA1;BP4;BP7,0.31194543838501,BP4;BP7;BA1,,,"This synonymous variant has a MAF of 0.002828 (0.2828%, 61/21570, 43140 alleles) in the African (gnomAD) cohort is ≥ 0.0015 (0.15%) (BA1). It is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -0.12 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP4, and BP7." -NM_001754.4(RUNX1):c.423G>A,BS1;BP4;BP7,PM1;PM2,1.53935885429382,BP7;BP4,PM1;PM2,BS1,PM2;BP4;BP6;BP7,0.361729860305786,BP7;BP4,BS1,PM2;BP6,BS1;BP4;BP7,0.313875436782837,BS1;BP4;BP7,,,"The MAF of the NM_001754.4(RUNX1):c.423G>A (p.Ser141=) variant is 0.0001633 (0.016%, 5/30614 alleles, 251394 alleles) in the South Asian cohort (gnomAD), which is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created (BP4). In addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score: -1.49 < 0.1 [-14.1;6.4]) (BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BS1, BP4, and BP7." -NM_000546.5(TP53):c.704A>G,BS1;BS2;BS3;BS4;BP2;BP4,PM1;PM2,1038.8517036438,BS1;BS2,PM1;PM2,BS4;BP4,PM1;PM2;PP3;BP6,0.399460077285767,,BP2;BP4;BS3;BS2;BS4;BS1,PM2;BP6;PM1;PP3,BS1;BS2;BS3;BS4;BP2;BP4,0.297839879989624,BP2;BS3;BS2;BS4;BS1;BP4,,,"This variant has a minor allele frequency of 0.0003175 (0.03%, 41/129,118 alleles) in the European (non-Finnish) subpopulation of the gnomAD cohort (BS1). The variant has a BayesDel score < 0.16 and Align GVGD (Zebrafish) is Class C0 or Class C15 (BP4). Additionally, transactivation assays show retained function according to Kato, et al. and there is no evidence of a dominant negative effect or loss of function according to Giacomelli, et al. (BS3; PMID: 12826609, 30224644). This variant also segregates to the opposite side of a family who meets Li-Fraumeni syndrome criteria. (BS4; PMID: 17318340). The proband in this same family has a pathogenic variant (TP53 c.560-1G>A) in trans with this variant. (BP2; PMID: 17318340). Finally, this variant has been observed in at least 4 60+ year old females without a cancer diagnosis (BS2_Supporting; FLOSSIES database - https://whi.color.com).In summary, TP53 c.704A>G; p.Asn235Ser meets criteria to be classified as benign for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: BS1, BP4, BS3, BS4, BP2, BS2_Supporting." -NM_000546.5(TP53):c.935C>G,BS1;BS3;BP4,PM1;PM2,1030.96031284332,BP4;BS1,PM1;PM2,BS3,PM1;PM2;PP3;BP6;BS2,0.386345863342285,,BS3;BP4;BS1,PM2;BP6;PP3;BS2;PM1,BS1;BS3;BP4,0.315615653991699,BS1;BP4;BS3,,,"This variant has an allele frequency of 0.0003605 (0.03%, 9/24,966 alleles) in the African subpopulation of the gnomAD cohort (BS1). This variant also has a BayesDel score < 0.16 and Align GVGD (Zebrafish) is Class C0 or Class C15 (BP4). Additionally, transactivation assays show retained function according to Kato, et al. and there is no evidence of a dominant negative effect or loss of function according to Giacomelli, et al. (BS3; PMID: 12826609, 30224644). In summary, TP53 c.935C>G; p.Thr312Ser meets criteria to be classified as benign for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: BS1, BP4, BS3." -NM_000546.5(TP53):c.869G>A,BS1;BS2;BS3;BP4,PM1;PM2,1062.64483118057,BP4;BS1,PM1;PM2,BS3;BS2,PM1;PM2;BP6;BS2,0.402278184890747,BS2,BS3;BP4;BS1,PM2;BP6;PM1,BS1;BS2;BS3;BP4,0.297675371170044,BS1;BP4;BS3;BS2,,,"This variant has a minor allele frequency of 0.0003583 (0.03%, 9/25,120 alleles) in the European Finnish subpopulation of the gnomAD cohort (BS1). Transactivation assays show super transactivation function according to Kato, et al. and there is no evidence of a dominant negative effect or loss of function according to Giacomelli, et al. (BS3; PMID: 12826609, 30224644). Additionally, this variant has a BayesDel score < 0.16 and Align GVGD (Zebrafish) is Class C0 or Class C15 (BP4). Finally, this variant has been observed in at least 7 60+ year old females without a cancer diagnosis (BS2_Supporting; FLOSSIES database - https://whi.color.com). In summary, TP53 c.869G>A; p.Arg290His meets criteria to be classified as benign for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: BS1, BS3, BP4, BS2_Supporting." -NM_000441.2(SLC26A4):c.1708-18T>A,BA1;BP4;BP7,PM1;BS1;BS2,2.56100249290466,BP7;BA1,PM1;BS1;BS2,,,0,,,,BA1;BP4;BP7,0.300298929214477,BP4;BP7;BA1,,,"The filtering allele frequency (the lower threshold of the 95% CI of 1456/25104) of the c.1708-18T>A variant in the SLC26A4 gene is 5.55% for European (Finnish) chromosomes by gnomAD v2.1.1, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). This silent variant in SLC26A4 is not predicted by the computational prediction analysis using MaxEntScan to impact splicing (BP7, BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP7, BP4." +Variant,Expected Criteria,AutoACMG Criteria,AutoACMG Prediction time,AutoACMG True Positives,AutoACMG False Negatives,AutoACMG False Positives,Intervar Criteria,Intervar Prediction time,Intervar True Positives,Intervar False Negatives,Intervar False Positives,Genebe Criteria,Genebe Prediction time,Genebe True Positives,Genebe False Positives,Genebe False Negatives,Comment,,, +4-113568536-G-GA,PVS1,PVS1;PM1;PM2,3.32929086685181,PVS1,PM1;PM2,,,0,,,,,0.268923759460449,,,PVS1,Gene: LARP7,,, +NM_004360.3:c.1085delT,PVS1,PVS1;PM1,1.59775352478027,PVS1,PM1,,,0,,,,PVS1;PS4;PM2;PM5,0.307955503463745,PVS1,PS4;PM5;PM2,,Gene: CDH1; p.Val362GlyfsTer31; From Recommendation 07.09.2018,,, +NM_000152.4:c.525delT,PVS1,PVS1;PM1;PM2,1.64967465400696,PVS1,PM1;PM2,,,0,,,,PVS1;PM2;PM3;PP4,0.361843109130859,PVS1,PM3;PP4;PM2,,Gene: GAA; p.Glu176ArgfsTer45; From Recommendation 07.09.2018,,, +NM_000152.4:c.1987delC,PVS1,PVS1;PM1,1.53102111816406,PVS1,PM1,,,0,,,,PVS1;PM2;PP5,0.339899063110351,PVS1,PP5;PM2,,Gene: GAA; p.Gln663SerfsTer33; From Recommendation 07.09.2018,,, +NM_000152.4:c.2706delG,PVS1,PVS1;PM1,1.39712834358215,PVS1,PM1,,,0,,,,PVS1;PM2;PM3;PP4,0.344012498855591,PVS1,PM3;PP4;PM2,,Gene: GAA; p.Lys903ArgfsTer2; From Recommendation 07.09.2018,,, +NM_000218.2:c.567dupG,PVS1,PVS1;PM1,1.47669363021851,PVS1,PM1,,,0,,,,PVS1;PM2;PP5,0.334547519683838,PVS1,PP5;PM2,,Gene: KCNQ1; p.Arg190AlafsTer14; From Recommendation 07.09.2018,,, +NM_000218.2:c.1343dupC,PVS1,PVS1;PM1;PM2,1.5736825466156,PVS1,PM1;PM2,,,0,,,,PVS1;PP5,0.353738069534302,PVS1,PP5,,Gene: KCNQ1; p.Glu449ArgfsTer14; From Recommendation 07.09.2018,,, +NM_000441.1:c.365dupT,PVS1,PVS1;PM1;PM2,1.56346273422241,PVS1,PM1;PM2,,,0,,,,PVS1;PM2;PM3;PP4,0.35863447189331,PVS1,PM3;PP4;PM2,,Gene: SLC26A4; p.Pro123SerfsTer4; From Recommendation 07.09.2018,,, +NM_206933.2:c.4338_4339delCT,PVS1,PVS1;PM1;PM2,1.48185229301453,PVS1,PM1;PM2,,,0,,,,PVS1;PM2;PM3;PP1;PP4,0.375017404556274,PVS1,PM3;PP1;PP4;PM2,,Gene: USH2A; p.Cys1447GlnfsTer29; From Recommendation 07.09.2018,,, +NM_206933.2:c.4510dupA,PVS1,PVS1,1.41564512252808,PVS1,,,,0,,,,PVS1;PM2;PM3;PP4,0.32335090637207,PVS1,PM3;PP4;PM2,,Gene: USH2A; p.Arg1504LysfsTer26; From Recommendation 07.09.2018,,, +NM_004004.5:c.235delC,PVS1,PVS1;PM1;PM2,1.57983469963074,PVS1,PM1;PM2,,,0,,,,PVS1;PS3;PM3;BS1,0.33725094795227,PVS1,PM3;PS3;BS1,,Gene: GJB2; p.Leu79CysfsTer3; From Recommendation 07.09.2018,,, +NM_004004.5:c.35delG,PVS1,PVS1;PM1;PM2,1.52198648452759,PVS1,PM1;PM2,,,0,,,,PVS1;PS4;PM3;BA1,0.296200752258301,PVS1,PM3;PS4;BA1,,Gene: GJB2; p.Gly12ValfsTer2; From Recommendation 07.09.2018,,, +NM_004004.5:c.167delT,PVS1,PVS1;PM1;PM2,1.42025852203369,PVS1,PM1;PM2,,,0,,,,PVS1;PM3;BA1,0.350803375244141,PVS1,PM3;BA1,,Gene: GJB2; p.Leu56ArgfsTer26; From Recommendation 07.09.2018,,, +NM_000277.1:c.822_832del,PVS1,PVS1;PM1,1.40451002120972,PVS1,PM1,,,0,,,,PVS1;PM2;PM3;PP4,0.305345773696899,PVS1,PM3;PP4;PM2,,Gene: PAH; p.Lys274AsnfsTer5; From Recommendation 07.09.2018,,, +NM_000277.2:c.632delC,PVS1,PVS1;PM1;PM2,1.58016014099121,PVS1,PM1;PM2,,,0,,,,PVS1;PM2;PM3;PP4,0.294129848480225,PVS1,PM3;PP4;PM2,,Gene: PAH; p.Pro211HisfsTer130; From Recommendation 07.09.2018,,, +NM_000314.6:c.50_51delAA,PVS1,PVS1;PM1,1.42956137657166,PVS1,PM1,,,0,,,,PVS1;PS4;PM2,0.290371179580688,PVS1,PS4;PM2,,PTEN,,, +NM_000277.2:c.47_48del,PVS1,PVS1;PM1,1.36341953277588,PVS1,PM1,,,0,,,,PVS1;PM2;PM3;PP4,0.317233800888062,PVS1,PM3;PP4;PM2,,Gene: PAH; p.Ser16Ter; From Recommendation 07.09.2018,,, +NM_000277.2:c.1147C>T,PVS1,PVS1;PM1,1.71908473968506,PVS1,PM1,,PVS1;PM2;PP3;PP5,0.364331007003784,PVS1,,PP3;PP5;PM2,PVS1;PM2;PM3;PP4,0.312084913253784,PVS1,PM3;PP4;PM2,,Gene: PAH; p.Gln383Ter; From Recommendation 07.09.2018,,, +NM_004360.3:c.1792C>T,PVS1,PVS1;PM1,1.67226600646973,PVS1,PM1,,PVS1;PM2;PP3;PP5,0.398955106735229,PVS1,,PP3;PP5;PM2,PVS1;PS2;PS4;PM2;PM5;PP1,0.355690956115723,PVS1,PM5;PP1;PM2;PS2;PS4,,Gene: CDH1; p.Arg598Ter; From Recommendation 07.09.2018,,, +NM_000314.6:c.1003C>T,PVS1,PVS1;PM1,1.74338698387146,PVS1,PM1,,PVS1;PM2;PP3;PP5,0.430862426757813,PVS1,,PP3;PP5;PM2,PVS1;PM2;PP5,0.325910568237305,PVS1,PP5;PM2,,PTEN,,, +NM_000152.4:c.1A>G,PVS1,PVS1;PM1,1.74510979652405,PVS1,PM1,,PM2;PP5,0.356374740600586,,PVS1,PP5;PM2,PVS1;PS1;PM2;PP5,0.310552835464477,PVS1,PS1;PP5;PM2,,Gene: GAA; p.Met1Val; From Recommendation 07.09.2018,,, +NM_000218.2:c.2T>C,PVS1,PM1,1.71596670150757,,PM1,PVS1,PM2;PP3,0.358755111694336,,PVS1,PP3;PM2,PVS1;PM2,0.302855968475342,PVS1,PM2,,Gene: KCNQ1; p.Met1Thr; From Recommendation 07.09.2018,,, +NM_000277.2:c.1A>G,PVS1,PM1;PP3;BP4,1.64721179008484,,PM1;BP4;PP3,PVS1,PS3;PM2;PP3;PP5,0.359246492385864,,PVS1,PP3;PP5;PS3;PM2,PS3;PM2;PM3;PP4,0.303873777389526,,PM3;PS3;PP4;PM2,PVS1,Gene: PAH; p.Met1Val; From Recommendation 07.09.2018,,, +NM_000314.6:c.3G>T,PVS1,PM1,1.72468209266663,,PM1,PVS1,PM2;PP3,0.361842393875122,,PVS1,PP3;PM2,PVS1;PS1;PM2,0.291746616363525,PVS1,PS1;PM2,,Gene: PTEN; p.Met1Ile; From Recommendation 07.09.2018,,, +NM_176795.4(HRAS):c.173C>T,PS1;PS4;PM1;PM2;PM6;PP2;PP3,PM1;PP3;BP4,189.004821538925,PP3;PM1;PM2,BP4,PP2;PS1,PM1;PM2;PP3;PP5,0.4151291847229,PP3;PM2;PM1,PS1;PS4;PP2;PM6,PP5,PM1;PM2;PP3;PP5,0.320986270904541,PP3;PM1;PM2,PP5,PP2;PM6;PS4;PS1,from ClinGen https://erepo.clinicalgenome.org/evrepo/ui/classification/4fa14d9d-3bce-4dd8-affa-771b6298c4fc,,, +NM_000277.2(PAH):c.503delA,PVS1;PM2;PP4,PVS1;PM1;PM2,1.39300084114075,PM2;PVS1,PM1,PP4,,0,,,,PVS1;PM2;PP4,0.311551809310913,PVS1;PP4;PM2,,,"PAH-specific ACMG/AMP criteria applied: PVS1: Frameshift variant; PM2: Extremely low frequency. ExAC MAF: 0.00001.; PP4: Detected in PKU patient in international phase II clinical trial for sapropterin. (PMID:23430918). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PVS1, PM2, PP4).",,, +NM_000277.1(PAH):c.814G>T,PVS1;PM2;PP4,PVS1;PM1;PM2,1.78998494148254,PM2;PVS1,PM1,PP4,PVS1;PM2;PP3;PP5,0.366233825683594,PVS1;PM2,PP4,PP3;PP5,PVS1;PM2;PP4,0.341337919235229,PVS1;PP4;PM2,,,"PAH-specific ACMG/AMP criteria applied: PM2: Absent from 1000G, ESP. Extrememly low frequency in ExAC, gnomAD (MAF= 0.00006, 0.0003093); PVS1: Nonsense variant. Predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay.; PP4: G272X found on one allele of a patient with classic PKU (PMID:1975559). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PVS1, PP4).",,, +NM_000277.1(PAH):c.1162G>A,PS3;PM2;PM3;PP3;PP4,PM1;PM2;PM5;PP3;BP4,7.61773657798767,PM2;PP3,PM1;PM5;BP4,PS3,PM1;PM2;PP3;PP5;BP1,0.374915599822998,PP3;PM2,PP4;PS3;PM3,PP5;BP1;PM1,PS3;PM2;PM3;PP3;PP4,0.311354875564575,PM3;PP3;PS3;PM2;PP4,,,"PAH-specific ACMG/AMP criteria applied: PM2: Extremely low in ExAC and 1000 genomes (PMID:9860305); PS3: PAH activity in COS cell expression system 15% (PMID:9860305); PM3: Compound het with severe mutation (PMID:9860305); PP3: ; PP4: Reported in patient with classic PKU (PMID:9860305). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PS3, PM3, PP3, PP4).",,, +NM_000257.3(MYH7):c.3036C>T,BA1;BP7,PM2;BP7,2.65372490882874,BP7,PM2,BA1,PM2;BP4;BP6;BP7,0.369901895523071,BP7,BA1,BP6;BP4;PM2,BA1;BP7,0.317893028259277,BP7;BA1,,,"The filtering allele frequency of the c.3036C>T (p.Ala1012=) silent variant in the MYH7 gene is 0.7% (137/16512) of South Asian chromosomes by the Exome Aggregation Consortium (http://exac.broadinstitute.org), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Inherited Cardiomyopathy Expert Panel (BA1, BP7; PMID:29300372).",,, +NM_000156.6(GAMT):c.279C>T,BA1;BP4;BP7,PM2;BP7,2.99034929275513,BP7;BP4,PM2,BA1,BP4;BP6;BP7,0.342584133148193,BP7;BP4,BA1,BP6,BA1;BP4;BP7,0.314168930053711,BP4;BP7;BA1,,,"The NM_000156.6:c.279C>T (p.Asp93=) is a synonymous variant in GAMT that is predicted to not impact splicing by SpliceAI and VarSeak, and the nucleotide is not highly conserved (BP4, BP7). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00484 (87/17976 alleles) in the East Asian population, which is higher than the ClinGen CCDS VCEP’s threshold for BA1 (>0.003), and therefore meets this criterion (BA1). This variant does not appear to have been previously reported in the published literature. It is noted in ClinVar (Variation ID 137434). In summary, this variant meets the criteria to be classified as benign for GAMT deficiency. GAMT-specific ACMG/AMP codes met, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): BA1, BP4, BP7.(Classification approved by the ClinGen CCDS VCEP on June 6, 2022).",,, +NM_004700.3(KCNQ4):c.720C>G,BP4;BP7,PM1;BP7,2.16768383979797,BP7,PM1,BP4,PM2;BP4;BP6;BP7,0.383844614028931,BP7;BP4,,BP6;PM2,BP4;BP7,0.323836803436279,BP4;BP7,,,"The silent p.Thr240= variant in KCNQ4 is not predicted by computational tools to impact splicing (BP7. BP4). The variant is absent from the Genome Aggregation Database (http://gnomad.broadinstitute.org), however this is not considered evidence against a likely benign classification. In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied: BP7, BP4.",,, +NM_004985.4(KRAS):c.451-14T>C,BP4;BP7,PM1;PM2;BP7,2.11770963668823,BP7,PM1;PM2,BP4,,0,,,,BP4;BP7,0.302630424499512,BP4;BP7,,,"The c.451-14T>C variant in KRAS has been seen in 3 cases undergoing RASopathy panel testing (PS4 not met; LMM, GeneDx internal data; GTR ID: 26957, 21766; ClinVar SCV000170023.9, SCV000198459.4) is an intronic variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Computational prediction tools and conservation analysis suggest that the variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as likely benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BP4, BP7.",,, +NM_005343.3(HRAS):c.510G>A,BP4;BP5;BP7,PM2;BP7,1.92048192024231,BP7,PM2,BP4,PM2;BP4;BP6;BP7,0.363871812820435,BP7;BP4,BP5,BP6;PM2,BS1;BS2;BP4;BP6;BP7,0.339710474014282,BP4;BP7,BS1;BS2;BP6,BP5,"The c.510G>A (p.Lys170=) variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Computational prediction tools and conservation analysis suggest that the p.Lys170= variant does not impact the protein (BP4).This variant has been identified in a patient with an alternate molecular basis for disease (BP5; LMM and GeneDx internal data; GTR ID's: 21766, 26957; ClinVar SCV000062144; SCV000168832). In summary, this variant meets criteria to be classified as likely benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BP7, BP5, BP4.",,, +NM_004333.4(BRAF):c.111G>A,BP5;BP7,PM2;BP7,2.05794048309326,BP7,PM2,BP5,PM2;BP4;BP6;BP7,1.38652539253235,BP7,BP5,BP6;BP4;PM2,BP5;BP7,0.299437761306763,BP5;BP7,,,"The c.111G>A (p.Ser37=) variant in BRAF is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). This variant has been identified in a patient with an alternate molecular basis for disease (BP5; Partners LMM, GeneDx internal data, GTR ID's: SCV000197179.4, SCV000512270.5). In summary, this variant meets criteria to be classified as likely benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BP7, BP5.",,, +NM_000152.5(GAA):c.1332T>C,BS1;BP4;BP7,PM1;PM2;BP7,1.9147162437439,BP7;BS1,PM1;PM2,BP4,PM2;BP4;BP6;BP7,0.384311676025391,BP7;BP4,BS1,BP6;PM2,BS1;BP4;BP7,0.324812889099121,BS1;BP4;BP7,,,"The NM_000152.5:c.1332T>C (p.Pro444=) variant in GAA is a synonymous (silent) variant that is not predicted to impact splicing; the nucleotide is not highly conserved (PhyloP 100 way score is -2.4 (BP4, BP7). There is a ClinVar entry for this variant (Variation ID: 286018). In summary, this variant meets the criteria to be classified as likely benign for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases VCEP (Specifications Version 2.0): BS1, BP4, BP7.(Classification approved by the ClinGen Lysosomal Diseases VCEP, March 13, 2023).",,, +NM_001754.4(RUNX1):c.1317C>T,PM2;BP4;BP7,BP7,1.76365494728088,PM2;BP7,,BP4,PM2;BP4;BP6;BP7,0.358675479888916,BP7;BP4;PM2,,BP6,PM2;BP4;BP7,0.354830503463745,BP4;BP7;PM2,,,"Although this variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2), the synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score: -0.44 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7, PM2.",,, +NM_001754.4(RUNX1):c.36G>A,BP4;BP7,PM2;BP7,1.98864221572876,BP7,PM2,BP4,BP4;BP6;BP7,0.367478609085083,BP7;BP4,,BP6,BP4;BP7,0.310839653015137,BP4;BP7,,,"This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created. In addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score: -1.41 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7.",,, +NM_001754.4(RUNX1):c.843C>T,BP4;BP7,PM1;BP7,1.88208746910095,BP7,PM1,BP4,BP4;BP6;BP7,1.40275645256042,BP7;BP4,,BP6,BP4;BP7,0.325880765914917,BP4;BP7,,,"This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -2.38 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7.",,, +NM_005633.3(SOS1):c.1230G>A,BA1;BP4;BP5;BP7,PM2;BP7,1.99886441230774,BA1;BP7;BP4,PM2,BP5,BP4;BP6;BP7;BS1;BS2,0.367127656936645,BP7;BP4,BP5;BA1,BP6;BS1;BS2,BA1;BP4;BP5;BP7,0.294578552246094,BP4;BP5;BP7;BA1,,,"The c.1230G>A (p.Gln410=) variant in SOS1 has been identified in a patient with an alternate molecular basis for disease (BP5; Partners LMM internal data GTR Lab ID: 21766 ClinVar SCV000062189.5). This variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Computational prediction tools and conservation analysis suggest that the p.Gln410= variant does not impact the protein (BP4). The filtering allele frequency of the c.1230G>A (p.Gln410=) variant in the SOS1 gene is 4.69% for Latino chromosomes by the Exome Aggregation Consortium (580/11526 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP5, BP7, BP4.",,, +NM_004700.3(KCNQ4):c.825G>C,PM1;PM2;PM5;PP3,PM1;PP3;BP4,7.50642442703247,PM1;PM5;PP3,BP4,PM2,PM1;PM2;PP3;PP5,0.399600028991699,PP3;PM2;PM1,PM5,PP5,PM1;PM2;PM5;PP3,0.332918882369995,PP3;PM1;PM5;PM2,,,"The c.825G>C variant in KCNQ4 is a missense variant predicted to cause substitution of tryptophan by cysteine at amino acid 275 (p.Trp275Cys). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.928, which is above the threshold of 0.7, evidence that correlates with impact to KCNQ4 function (PP3). This variant has been reported in one individual with hearing loss and segregated in an affected first degree relative (SCV000712456.1). This variant is located within the pore-forming intramembrane region (amino acids 271-292) where many variants that cause autosomal dominant hearing loss are located and is defined as a critical functional domain by the ClinGen Hearing Loss VCEP (PM1; PMID: 23717403). A different missense variant at the same codon (p.Trp275Arg) has been classified as Pathogenic by the ClinGen Hearing Loss VCEP (PM5; ClinVar Variation ID 204597, PMID: 25116015). In summary, this variant is classified as Likely Pathogenic for autosomal dominant sensorineural hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM2_Supporting, PP3, PM1, PM5. (VCEP specifications version 2; 10.18.2023).",,, +NM_000257.3(MYH7):c.1157A>G,PS4;PM1;PM2;PM6;PP3,PM1;PP3;BP4,7.99599170684814,PM1;PP3;PM2,BP4,PM6,PM1;PM2;PP2;PP3;PP5;BP1,0.816510677337647,PP3;PM2;PM1,PS4;PM6,PP5;PP2;BP1,PS4;PM1;PM2;PM6;PP3,0.351853609085083,PM6;PP3;PM2;PM1;PS4,,,"The NM_000257.4(MYH7):c.1157A>G (p.Tyr386Cys) variant has been reported as a de novo occurence in 2 infants with early-onset/severe cardiomyopathy that presented with variable features (1 with features of HCM and RCM, and 1 with features of HCM and LVNC that progressed to DCM; Lakdawala 2012 PMID:22464770; Greenway 2012 PMID:23170025; Alfares 2015 PMID:25611685; LMM pers. comm.) and in an additional case with RCM (age unknown; GeneDx pers. comm.). Collectively, this data meets criteria for PS4_Supporting and PM6. This variant was absent from large population studies (PM2; gnomAD v2.1.1, http://gnomad.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be associated with HCM (PM1; Walsh 2017 PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for complex cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (Kelly 2018 PMID:29300372): PS4_Supporting, PM6, PM2, PM1, PP3.",,, +NM_005343.3(HRAS):c.175G>A,PS4;PM1;PM2;PP1;PP2;PP3,PM1,191.677925348282,PP2;PM1,,PM2;PP3,PM1;PM2;PP3;PP5,0.369871139526367,PP3;PM2;PM1,PS4;PP2;PP1,PP5,PS4;PM1;PM2;PP1;PP2;PP3,0.479533195495605,PP3;PP2;PP1;PM2;PM1;PS4,,,"The c.175G>A (p.Ala59Thr) variant in HRAS has been identified in at least 3 independent occurrences in patients with a RASopathy (PS4_Moderate; GeneDx, Partners LMM, Invitae internal data; ClinVar SCV000198374, SCV000950586). The p.Ala59Thr variant segregated with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Partners LMM internal data). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of HRAS (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ala59Thr variant may impact the protein (PP3). The variant is located in the HRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM1, PM2, PS4_Moderate, PP1, PP2, PP3.",,, +NM_030662.3(MAP2K2):c.400T>C,PS4;PM1;PM2;PP2;PP3,PM1;PP3;BP4,264.390161752701,PP2;PM1;PP3,BP4,PM2,PM1;PM2;PP3;PP5,0.392758131027222,PP3;PM2;PM1,PS4;PP2,PP5,PS4;PM1;PM2;PP2;PP3,0.383073329925537,PP3;PP2;PM2;PM1;PS4,,,"The c.400T>C (p.Tyr134His) variant in MAP2K2 was absent from large population studies (PM2). It has been identified in 3 patients with Cardiofaciocutaneous syndrome and 1 with Noonan syndrome (PS4_Moderate; SCV000063166.5, Hopital Universitaire Robert Debre internal data, PMIDs: 18042262, 27763634)Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K2 (PM1; PMID 29493581). Moreover, a different pathogenic missense variant (p.Tyr134Cys) has been previously identified at this codon of MAP2K2 which may indicate that this residue is critical to the function of the protein (PM5 not met; ClinVar 177868). The variant is located in the MAP2K2 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Tyr134His variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM2, PS4_Moderate, PM1, PP2, PP3.",,, +NM_004333.4(BRAF):c.739T>G,PS4;PM1;PM2;PP2;PP3,PM1;PM5;PP3;BP4,13.155256986618,PP2;PM1;PP3;PM2,PM5;BP4,PS4,PM1;PM2;PP3;PP5,0.371227264404297,PP3;PM2;PM1,PS4;PP2,PP5,PS4;PM1;PM2;PP2;PP3,0.347076892852783,PP3;PP2;PM2;PM1;PS4,,,"The c.739T>G (p.Phe247Val) variant in BRAF has been identified in at least 2 independent occurrences in patients with clinical features of a RASopathy (PS4_Supporting; Partners LMM, GeneDx internal data; GTR Lab IDs 21766, 26957; ClinVar SCV000061624.5, SCV000330320.6). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). A different pathogenic missense variant (p.Phe247Leu) has been previously identified at this codon of BRAF which may indicate that this residue is critical to the function of the protein (PM5 not usable due to PM1 application; ClinVar 180784, 55793). Computational prediction tools and conservation analysis suggest that the p.Phe247Val variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM2, PM1, PP2, PP3.",,, +NM_001754.4(RUNX1):c.316T>A,PS3;PM1;PM2;PP3,,1.46527314186096,PM2,,PM1;PP3,PM1;PM2;PP3;PP5;BP1,0.371410608291626,PP3;PM2;PM1,PS3,PP5;BP1,PS3;PM1;PM2;PP3,0.32424259185791,PP3;PM1;PS3;PM2,,,"The NM_001754.4:c.316T>A (p.Trp106Arg) variant affects one of the residues (AA 105-204) within the RHD (PM1_Supporting). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2). Transactivation assays demonstrating altered transactivation (<20% of wt, and/or reduced to levels similar to well-established pathogenic variants such as R201Q or R166Q) AND data from secondary assay demonstrate altered DNA binding. (PS3; PMID: 25840971). This missense variant has a REVEL score >0.75 (0.976) (PP3). All patients reported in literature with this variant were not confirmed as germline variants (PMID: 21828118, PMID: 19282830, PMID: 25840971). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PS3, PM2, PP3, PM1_supporting.",,, +NM_001754.4(RUNX1):c.314A>C,PS4;PM1;PM2;PM5;PP3,,0.688652515411377,PM5;PP3,,PM1;PM2,PM1;PM2;PP3;PP5;BP1,0.364496469497681,PP3;PM2;PM1,PS4;PM5,PP5;BP1,PS4;PM1;PM2;PM5;PP3,0.3201744556427,PM5;PP3;PM2;PM1;PS4,,,"The NM_001754.4:c.314A>C (p.His105Pro) variant affects one of the residues (AA 105-204) within the RHD (PM1_Supporting). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2). This missense variant has a REVEL score >0.75 (0.953) (PP3). This variant is a missense change at the same residue (p.His105Pro) where a different missense change has been previously established as a likely pathogenic variant (NM_001754.4:c.315C>A (p.His105Glu)) based on MM-VCEP rules for RUNX1 and RNA data or agreement in splicing predictors (SSF and MES) show no splicing effects (PM5_Supporting). This variant has been reported in one proband meeting at least one of the RUNX1-phenotypic criteria (PS4_ Supporting; SCV000807773.1). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM2, PP3, PM1_supporting, PM5_supporting, PS4_supporting.",,, +NM_001754.4:c.315C>A,PS3;PM1;PM2;PP3,,0.717023372650147,PM2;PP3,,PM1;PS3,PM1;PM2;PP3;PP5;BP1,0.364284753799438,PP3;PM2;PM1,PS3,PP5;BP1,PS3;PM1;PM2;PP3,0.311601400375366,PP3;PM1;PS3;PM2,,,"The NM_001754.4:c.315C>A (p.His105Gln) variant affects one of the residues (AA 105-204) within the RHD (PM1_Supporting). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2). Transactivation assays demonstrating altered transactivation (<20% of wt, and/or reduced to levels similar to well-established pathogenic variants such as R201Q or R166Q) AND data from secondary assays demonstrate altered DNA binding and functional consequences in mouse model. (PS3; PMID: 22318203; PMID: 25840971). This missense variant has a REVEL score >0.75 (0.901) (PP3). All patients reported in literature with this variant were not confirmed as germline variants (PMID 22318203, PMID 29722345, PMID 25840971, PMID 24030381, PMID 19282830). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PS3, PM2, PP3, PM1_supporting.",,, +NM_002834.4(PTPN11):c.782T>A,PS4;PM1;PP2,,0.656793832778931,PM1,,PP2,PM1;PM2;PP3;PP5,0.401057004928589,PM1,PS4;PP2,PP3;PP5;PM2,PS4;PM1;PP2,0.317038059234619,PP2;PM1;PS4,,,"The c.782T>A (p.Leu261His) variant in PTPN11 is present in 1/6064 “other” alleles in gnomAD v2.1.1; however, it is absent from gnomAD v3 (PM2 not met). It has been identified in 7 independent occurrences in patients with clinical features of a RASopathy (PS4; PMIDs: 28074573, 22253195, 23756559). A functional assay performed on this variant does not meet approved RASopathy VCEP guidelines for criteria application (PS3 not met; PMID: 28074573). This variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot of PTPN11 (PM1; PMID 29493581). PTPN11 has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant RASopathy based on the RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4, PM1, PP2.",,, +NM_004333.6(BRAF):c.793G>C,PS4;PM1;PM2;PM6;PP2;PP3,,0.633267164230347,PM1;PP3,,PP2;PM2,PM1;PM2;PP3;PP5,0.364014625549316,PP3;PM2;PM1,PS4;PP2;PM6,PP5,PS4;PM1;PM2;PM6;PP2;PP3,0.310089111328125,PM6;PP3;PP2;PM2;PM1;PS4,,,"The c.793G>C (p.Gly265Arg) variant in BRAF was absent from large population studies (PM2; gnomad.broadinstitute.org). It was observed as a de novo occurrence in one proband diagnosed with a RASopathy (PM6, PS4_Supporting; Laboratory for Molecular Medicine internal data, ClinVar SCV000061628.5). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Gly265Arg variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant RASopathy. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM1, PM2, PM6, PP2, PP3.",,, +NM_005633.3(SOS1):c.1276C>A,PS4;PM1;PM2;PP2;PP3,,0.642684936523438,PM2;PP3,,PP2;PM1,PM1;PM2;PP3,0.411989450454712,PP3;PM2;PM1,PS4;PP2,,PS4;PM1;PM2;PP2;PP3,0.332223653793335,PP3;PP2;PM2;PM1;PS4,,,"The c.1276C>A (p.Gln426Lys) variant in SOS1 was absent from large population studies (PM2; gnomad.broadinstitute.org). It was observed in 1 individual with a diagnosis of Noonan syndrome (PS4_Supporting; GeneDx internal data, ClinVar SCV000808402.1). SOS1 has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of SOS1 (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Gln426Lys variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID: 29493581): PM1, PM2, PP2, PP3, PS4_Supporting.",,, +NM_000546.5(TP53):c.396G>C,PS3;PM1;PM2;PP3,,0.727421998977661,PM1;PP3,,PM2;PS3,PM1;PM2;PP3;PP5,0.376925945281982,PP3;PM2;PM1,PS3,PP5,PS3;PM1;PM2;PP3,0.305541515350342,PP3;PM1;PS3;PM2,,,"Transactivation assays show a low functioning allele according to Kato, et al. and there is evidence of a dominant negative effect and loss of function according to Giacomelli, et al. (PS3; PMID: 12826609, 30224644). This variant has a BayesDel score > 0.16 and Align GVGD (Zebrafish) is Class 65 (PP3_Moderate). This variant has >10 observations as a somatic hotspot variant in tumors (PM1; cancerhotspots.org v(2)). This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). In summary, TP53 c.396G>C (p.Lys132Asn) meets criteria to be classified as likely pathogenic for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: PS3, PP3_Moderate, PM1, PM2_Supporting.",,, +NM_001754.4(RUNX1):c.485G>A,PM1;PM2;PM5;PP3,,0.759462118148804,PM2;PP3,,PM1;PM5,PM1;PM2;PP3;PP5;BP1,0.374862909317017,PP3;PM2;PM1,PM5,PP5;BP1,PS4;PM1;PM2;PM6;PP2,0.325146436691284,PM1;PM2,PP2;PM6;PS4,PP3;PM5,"This missense variant has not been reported in gnomAD (v2 and v3) [PM2]. It has been reported as a germline variant by SCV001203102.1 in a proband (70s) with thrombocytopenia and anemia; however, the germline origins were not confirmed in this case and all other reports of the variant (PMID: 19808697, 22689681, 24523240, 24659740, 25592059, 26273060, 27220669, 27534895, 28659335, 28933735, 30373888, 31649132, 32045476, 32208489, COSMIC). The variant is located at a residue that directly contacts DNA (PMID: 11276260, 12377125, 12393679, 12807882, 19808697, 28231333) and is considered a hotspot residue (PMID: 31648317, 27294619, 23958918), especially from a somatic perspective (PMID: 32208489) [PM1]. Although this variant has not been functionally evaluated, computational evidence supports a deleterious effect of this variant [PP3] and another missense variant at the same residue (i.e. p.R162G) is classified as likely pathogenic by the ClinGen MM-VCEP [PM5_supporting]. In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM1, PM2, PM5_supporting, and PP3.",,, +NM_000277.2(PAH):c.1092_1094del,PM2;PM3;PM4;PP4,PM1;PM4,1.44384956359863,PM2;PM4,PM1,PP4,,0,,,,PM1;PM2;PM5;PP3,0.319685697555542,PM2,PP3;PM1;PM5,PM3;PP4;PM4,"The c.1092_1094delTCT variant in PAH has been previously reported as a single variant, found in trans with the Pathogenic variant (per internal PAH ClinGen Working Group classification, see ClinVar allele ID 15635) p.Gly272Ter in one proband with classic PKU (PMID: 1975559); phase was confirmed via parental testing (PM3). Apart from stating that the proband was identified via newborn screening further detail is provided regarding the proband’s phenotype, including whether BH4 deficiency was formally excluded (PP4?). The variant is a protein-length changing variant in a non-repeat region (PM4). It is absent from control databases including ethnically matched individuals, including gnomAD/ExAC, 1000 Genomes, and ESP (PM2).",,, +NM_000277.2(PAH):c.1092_1106del,PM2;PM3;PM4;PP4,PM1;PM4,1.39032506942749,PM2;PM4,PM1,PM3,,0,,,,PM2;PM3;PM4;PP4,0.324632167816162,PM3;PP4;PM4;PM2,,,"The c.1092_1106del (p.Leu365_Leu369del) variant in PAH has been reported in 1 individual with PKU (PP4; PMID: 1363837) in trans with pathogenic variant p.R408W (PM3). This variant is absent in population databases (PM2). This variant is a 15 bp in-frame deletion in exon 11 (PM4). In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4, PM2, PM3, PM4.",,, +NM_000277.1(PAH):c.208_210delTCT,PS3;PM2;PM3;PM4;PP4,PM1;PM2;PM4,1.38096714019775,PM2;PM4,PM1,PP4,,0,,,,PM2;PM3;PM4;PP4,0.313969135284424,PM3;PP4;PM4;PM2,,PS3,"PAH-specific ACMG/AMP criteria applied: PP4: Phe>120 umol/L with PKU (PMID:25456745); PM3: In trans with: c.842+2T>A (P, ClinGen) (PMID:25456745); PS3: 0% in BioPKU; PM2: Extremely low frequency. ExAC MAF=0.00012; PM4: In frame deletion. In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PP4, PM3, PS3, PM2, PM4).",,, +NM_000277.2(PAH):c.865G>C,PS1;PM2;PM3;PP3;PP4,PS1;PM1;PP3;BP4,7.5553765296936,PS1;PP3,PM1;BP4,PM2,PM1;PM2;PP3;PP5;BP1,0.359306812286377,PP3;PM2,PS1;PP4;PM3,PP5;BP1;PM1,PS3;PM2;PM3;PM4;PP4,0.320562839508057,PM3;PP4;PM2,PS3;PM4,PP3;PS1,"The c.865G>C (p.Gly289Arg) variant in PAH is absent from population databases and predicted deleterious with in silico prediction software. This is the same amnio acid change as a previously established pathogenic variant (c.865G>A; p.Gly289Arg). It has been identified in trans with a pathogenic variant (R155C, curated by the PAH EP), and a defect in BH4 metabolism was excluded (PMID: 22921945). In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PS1, PM2, PM3, PP3.",,, +NM_004333.4(BRAF):c.735A>T,PS1;PS4;PM1;PM2;PM6;PP2;PP3,PS1;PM1;PP3;BP4,8.01120638847351,PP3;PM1;PS1;PM2,BP4,PP2;PM6,PM1;PM2;PP3;PP5,0.35802173614502,PP3;PM2;PM1,PS1;PS4;PP2;PM6,PP5,PS1;PM2;PM3;PP3;PP4,0.320266723632812,PP3;PS1;PM2,PM3;PP4,PP2;PM1;PM6;PS4,"The c.735A>T p.Leu245Phe variant in BRAF has been identified in at least 2 independent occurrences, one of which was de novo, in patients with clinical features of a RASopathy (PM6, PS4_Supporting; Partners LMM, University Magdeburg internal data; GTR Lab IDs: 21766, 506381 PMID: 19206169, 22190897). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that the p.Leu245Phe variant may impact the protein (PP3). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Of note, the p.Leu245Phe change has also been reported as a consequence of the c.735A>C variant in BRAF, which has been classified as pathogenic and therefore supports that this residue may be critical to protein function (PS1; ClinVar ID: 40347). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM6, PM1, PM2, PS1, PP2, PP3.",,, +NM_005633.3(SOS1):c.1656G>T,PS1;PS2;PS4;PM1;PM2;PP2;PP3,PS1;PM1,14.6982409954071,PM1;PS1;PM2,,PP2;PP3,PM1;PM2;PP3;PP5,0.531394004821777,PP3;PM2;PM1,PS1;PS4;PP2;PS2,PP5,PS1;PS4;PM1;PM2;PM6;PP2;PP3,0.317075967788696,PP3;PP2;PM2;PM1;PS4;PS1,PM6,PS2,"The c.1656G>T (p.Arg552Ser) variant in SOS1 has been reported as a confirmed de novo occurrence in one patient and 2 other probands with clinical features of a RASopathy (PS2, PS4_Moderate; PMID 17586837, 18854871). Of note, one of these cases was an affected mother-child duo (PP1 not met; PMID: 17586837). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). This amino acid residue has been designated as a hotspot. These variants would have received PM5_Strong but the RAS EP decided that PM1 and PM5 cannot be used simultaneously and therefore this rule has been upgraded with expert judgement (PM1_Strong). Of note, the p.Arg552Ser variant in SOS1 has also been a consequence of the c.1656G>C nucleotide change which has been classified as pathogenic (PS1; ClinVar ID 12872). Computational prediction tools and conservation analysis suggest that the p.Arg552Ser variant may impact the protein (PP3). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2, PS1, PM1_Strong, PM2, PS4_Moderate, PP2, PP3.",,, +NM_000277.3(PAH):c.865G>A,PS1;PM2;PM3;PP3;PP4,,0.739319324493408,PP3,,PS1;PM2,PM1;PM2;PP3;PP5;BP1,0.376642465591431,PP3;PM2,PS1;PP4;PM3,PP5;BP1;PM1,PS1;PS2;PS4;PM1;PM2;PP2;PP3,0.318098068237305,PP3;PS1;PM2,PP2;PM1;PS2;PS4,PM3;PP4,"This c.865G>A (p.Gly289Arg) variant in PAH was reported in 2 patients with PAH deficiency (PMID: 27121329) detected with the pathogenic variant p.Gly272* and the likely pathogenic variant p.Arg155Cys. DHPR activity, biopterin and/or pteridine analysis was performed to rule out other causes of hyperphenylalaninemia. This variant has the same amino acid change as a previously established pathogenic variant in ClinVar (Variation ID: 102882). This variant is absent in population databases. Computational evidence for this missense variant supports a deleterious effect. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PS1, PM2, PP4_moderate, PM3, PP3.",,, +NM_000540.2(RYR1):c.1021G>C,PS1;PS3;PS4;PM1;PP1;PP3,,0.776044130325317,PM1;PP3,,PS1;PS3,PM1;PM2;PP3,0.412060976028442,PP3;PM1,PS1;PS4;PS3;PP1,PM2,PS1;PM2;PM3;PP3;PP4,0.306127786636352,PP3;PS1,PM3;PP4;PM2,PP1;PS4;PM1;PS3,"This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions. This sequence variant predicts a substitution of Glycine with Arginine at codon 341 of the RYR1 protein, p.(Gly341Arg), c.1021G>C. This variant was not present in a large population database (gnomAD) at the time this variant was interpreted. This variant has been reported in five unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, four of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (if the proband was unavailable for testing, a positive diagnostic test result in a mutation-positive relative was counted), PS4_Moderate (PMID:12059893, PMID:16163667, PMID:30236257 ). This variant segregates with MHS in five individuals/families, PP1_Moderate (PMID:12059893, PMID:12411788). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:9334205). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, use PM1_Supporting to avoid overweighting with PS1 (PMID: 21118704). Another variant has been assessed as pathogenic occurs at this codon, p.(Gly341Arg, c.1021G>A), PS1. This variant segregates with MHS in two individuals (PMID:12059893). A REVEL score >0.85 (0.876) supports a pathogenic status for this variant, PP3_Moderate. This variant has been classified as Pathogenic. Criteria implemented: PS4_Moderate, PS3_Moderate, PM1_Supporting, PS1, PP3_Moderate. ",,, +NM_000540.2(RYR1):c.742G>C,PS1;PS3;PS4;PM1;PP1;PP3,,0.693361520767212,PM1;PP3,,PS1;PS3,PM1;PM2;PP3;PP5,0.374715566635132,PP3;PM1,PS1;PS4;PS3;PP1,PP5;PM2,PS1;PS3;PS4;PM1;PP1;PP3,0.33376669883728,PP3;PS3;PP1;PM1;PS4;PS1,,,"This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions.This sequence variant predicts a substitution of glycine with arginine at codon 248 of the RYR1 protein c.742G>C; p.(Gly248Arg). The maximum allele frequency for this variant among the six major gnomAD populations is EAS: 0.00005), a frequency consistent with pathogenicity for MHS. This variant has been reported in four unrelated individuals who have a personal or family history of a malignant hyperthermia reaction and a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted), PS4_Moderate (PMID:30236257, PMID:19346234). This variant segregates with MHS in five individuals/families, PP1_Moderate (PMID:30236257, PMID:19346234, PMID:18564801). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:26115329, PMID:27857962). Another variant assessed as pathogenic occurs at this codon, c.742G>A; p.(Gly248Arg), PS1. This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, use PM1_Supporting to avoid overweighting with PS1 (PMID: 21118704).A REVEL score > 0.85 supports pathogenicity, PP3_Moderate. This variant has been classified as Pathogenic. Criteria implemented: PS4_Moderate, PS3_Moderate, PM1_Supporting, PS1, PP1_Moderate, PP3_Moderate.",,, +NM_001110792.2(MECP2):c.408G>C,PS1;PS3;PM1;PM2;PM6,,0.70138144493103,PM2,,PS1;PM1,PM1;PM2;PP3;BP1,0.38634181022644,PM2;PM1,PS1;PS3;PM6,PP3;BP1,PS1;PS3;PS4;PM1;PP1;PP3,0.346795082092285,PM1;PS3;PS1,PP3;PP1;PS4,PM6;PM2,"The c.372G>C (p.Leu124Phe) variant in MECP2 (NM_004992.3) occurs in the de novo state (biological parentage unconfirmed) in an individual with Rett syndrome (PMID 10991688) (PM6). The c.372G>C (p.Leu124Phe) variant occurs in the well-characterized methyl-DNA binding functional domain of the MECP2 gene (PM1). The c.372G>C (p.Leu124Phe) variant in MECP2 is absent from gnomAD (PM2_supporting). MECP2 heterochromatin binding assay and in vitro transcriptional repression assay have shown that this variant impacts protein function (PMID 12843318) (PS3_supporting). The c.372G>T variant in the MECP2 gene results in a p.Leu124Phe change that is a previously established pathogenic variant (internal database - Invitae) (PS1). In summary, the c.372G>C (p.Leu124Phe) variant in MECP2 is classified as Pathogenic for Rett syndrome based on the ACMG/AMP criteria (PS1, PM1, PM6, PM2_supporting, PS3_supporting).",,, +NM_001110792.2(MECP2):c.408G>T,PS1;PS2;PM1;PM2,,0.661284685134888,PS1;PM1,,PM2;PS2,PM1;PM2;PP3;BP1,0.358327388763428,PM2;PM1,PS1;PS2,PP3;BP1,PS1;PS3;PM1;PM2;PM6,0.300886869430542,PM1;PS1;PM2,PM6;PS3,PS2,"The c.372G>T (p.Leu124Phe) variant in MECP2 (NM_004992.3) occurs in the mosaic state in a male patient with a neurodevelopmental phenotype consistent with the MECP2 gene (internal database - Invitae) and therefore confirmed to be de novo (PS2). The c.372G>T (p.Leu124Phe) variant occurs in the well-characterized methyl-DNA binding functional domain of the MECP2 gene (PM1). The c.372G>T (p.Leu124Phe) variant in MECP2 is absent from gnomAD (PM2_supporting). The c.372G>C variant in the MECP2 gene results in a p.Leu124Phe change that is a previously established pathogenic variant (PMID 10991688, 12843318) (PS1). In summary, the c.372G>T (p.Leu124Phe) variant in MECP2 is classified as Pathogenic for Rett syndrome based on the ACMG/AMP criteria (PS1, PS2, PM1, PM2_supporting).",,, +NM_000162.5(GCK):c.523G>A,PS1;PS3;PS4;PM2;PP1;PP2;PP3;PP4,,0.63607668876648,PP2;PM2,,PS1;PS3;PP3,PM1;PM2;PP3,0.405667543411255,PP3;PM2,PP4;PP2;PS3;PS1;PS4;PP1,PM1,PS1;PS2;PM1;PM2,0.31352972984314,PS1;PM2,PS2;PM1,PP3;PS3;PP2;PP1;PS4;PP4,"The c.523G>A variant in the glucokinase gene, GCK causes an amino acid change of Gly to Arg at codon 210 (p.(Gly175Arg)) of NM_000162.5. GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2). This variant is also predicted to be deleterious by computational evidence, with a REVEL score of 0.965, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in 8 unrelated individuals with diabetes (PS4; PMID: 29944009, 20337973, 26552609, internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and three-generation, dominant family history of diabetes/hyperglycemia) (PP4_Moderate; internal lab contributors). This variant segregated with diabetes with 5 informative meioses in 4 families with diabetes (PP1_Strong; internal lab contributors). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, but the wild-type ATP Km is not between 0.4-0.65, and the p.Gly175Arg variant has Kcat/S0.5<0.5 (PS3_Supporting; PMID 10525657). The nucleotide change c.523G>C, which causes the same amino acid change, has been classified as pathogenic for MODY by the ClinGen MDEP (PS1). In summary, this variant meets the criteria to be classified as Pathogenic for GCK-MODY. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0, approved 6/7/2023) : PS4, PP1_Strong, PP4_Moderate, PS3_Supporting, PM2_Supporting, PP2, PP3, PS1.",,, +NM_000277.1(PAH):c.782G>C,PM2;PM3;PM5;PP3;PP4,,0.722711801528931,PM2,,PM5;PP3,PM1;PM2;PP3;PP5;BP1,1.38493967056274,PP3;PM2,PM5;PP4;PM3,PP5;BP1;PM1,PS1;PS3;PS4;PM2;PP1;PP2;PP3;PP4,0.31301736831665,PP3;PP4;PM2,PS3;PP2;PP1;PS4;PS1,PM3;PM5,"The PAH c.782G>C (p.Arg261Pro) variant has been reported in multiple affected individuals (PMID: 26666653, Bh4 deficiency not ruled out, PP4). It has been detected with 5 known pathogenic variants (PM3_S). It is absent from ExAC/gnomAD. Computational evidence supports a deleterious effect. Also, p.R261Q is interpreted as pathogenic. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM3_S, PM2, PM5, PP4, PP3.",,, +NM_000277.2(PAH):c.734T>C,PM3;PM5;PP4,PM1;PM2;PM5;PP3;BP4,7.8391854763031,PM5,PM1;BP4;PP3;PM2,PP4,PM1;PM2;PP3;PP5;BP1,0.376780271530151,,PM5;PP4;PM3,PP5;PM1;BP1;PP3;PM2,PM2;PM3;PM5;PP3;PP4,0.310577154159546,PM3;PM5;PP4,PP3;PM2,,"PAH-specific ACMG/AMP criteria applied: PM5: V245L Pathogenic; PP4_Moderate: Seen in at least 7 MHP patients. Exclusion of a defect in tetrahydrobiopterin metabolism. Upgraded per ClinGen Metabolic Workgroup. (PMID:7981714; PMID:9298832; PMID:9634518); PM3_VeryStrong: V245A detected with IVS-12nt1, R252W, L194P (both P/LP), R408W (Path). Upgraded per ClinGen SVI Workgroup (PMID:7981714; PMID:9298832; PMID:8088845). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM5, PP4_Moderate, PM3_VeryStrong).",,, +NM_000257.3(MYH7):c.2221G>T,PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5,7.95476245880127,PM1;PM5;PP3,,PM2;PP1,PM1;PM2;PP2;PP3;PP5;BP1,0.370798349380493,PP3;PM2;PM1,PS4;PM5;PP1,PP5;PP2;BP1,PM3;PM5;PP4,0.306227684020996,PM5,PM3;PP4,PP3;PP1;PM2;PM1;PS4,"The c.2221G>T (p.Gly741Trp) variant in MYH7 has been reported in >15 individuals with hypertrophic cardiomyopathy (PS4; PMID: 8533830; PMID:15856146; PMID:27532257; Partners LMM ClinVar SCV000203910.4; AGCMC Sydney ClinVar SCV000212638.1). This variant segregated with disease in 5 affected individuals (PP1_Moderate; PMID:15856146; AGCMC Sydney ClinVar SCV000212638.1). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2221G>C p.Gly741Arg - Variation ID 14098). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PM1; PM2; PM5; PP1_Moderate; PP3",,, +NM_000257.3(MYH7):c.2221G>C,PS4;PM1;PM2;PM5;PM6;PP1;PP3,PM1;PM5,7.46528601646423,PP3;PM1;PM5,,PM2;PP1,PM1;PM2;PP2;PP3;PP5;BP1,0.363935708999634,PP3;PM2;PM1,PS4;PM5;PM6;PP1,PP5;PP2;BP1,PS4;PM1;PM2;PM5;PP1;PP3,0.287145614624023,PM5;PP3;PP1;PM2;PM1;PS4,,PM6,"The c.2221G>C (p.Gly741Arg) variant in MYH7 has been reported in >12 individuals with hypertrophic cardiomyopathy (PS4; PMID:8483915; PMID:15563892; PMID:20031618; PMID:15358028; Partners LMM ClinVar SCV000059430.5; SHaRe consortium, PMID: 30297972). This variant has been identified as a de novo occurrence in 1 proband with hypertrophic cardiomyopathy (PM6; PMID:15563892). This variant segregated with disease in 3 affected individuals (PP1; PMID:8483915; Partners LMM ClinVar SCV000059430.5). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2221G>T p.Gly741Trp - Variation ID 177665). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PM1; PM2; PM5; PM6; PP1; PP3",,, +NM_000257.3(MYH7):c.2167C>T,PS4;PM1;PM2;PM5;PM6;PP1;PP3;BP2,PM1;PM2;PM5,8.01106882095337,PM1;PM5;PM2,,PM6;PP3,PS3;PM1;PM2;PP2;PP3;PP5;BP1,0.370083808898926,PP3;PM2;PM1,PM5;PM6;PS4;PP1;BP2,PP5;PP2;PS3;BP1,PS4;PM1;PM2;PM5;PM6;PP1;PP3,0.311627149581909,PM6;PM5;PP3;PP1;PM2;PM1;PS4,,BP2,"The c.2167C>T (p.Arg723Cys) variant in MYH7 has been reported in >20 individuals with hypertrophic cardiomyopathy (PS4; PMID:1430197; PMID:27532257; PMID:9829907; PMID:16199542; PMID:20359594; PMID:12707239; Partners LMM ClinVar SCV000059423.5; AGCMC Sydney ClinVar SCV000212630.1). Five of these probands carried additional variants in sarcomere genes (BP2; PMID:20359594; PMID:12707239; Partners LMM ClinVar SCV000059423.5). This variant has been identified as a de novo occurrence in 1 proband with hypertrophic cardiomyopathy (PM6; PMID:1430197). This variant segregated with disease in 7 affected individuals (PP1_Strong; PMID:9829907; Partners LMM ClinVar SCV000059423.5; AGCMC Sydney ClinVar SCV000212630.1). This variant was identified in 2/66738 European chromosomes (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2167C>G p.Arg723Gly - ClinVar Variation ID 42885). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. The benign evidence code BP2 was not considered to be in conflict with this conclusion given that presence of a second variant can be seen in individuals with cardiomyopathy and may contribute to the severity of disease. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_ Strong; PM1; PM2; PM5; PM6; PP3; BP2",,, +NM_000257.3(MYH7):c.2167C>G,PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5,7.95137643814087,PM1;PM5,,PM2;PP3,PM1;PM2;PP2;PP3;PP5;BP1,0.38297176361084,PM1;PM2;PP3,PS4;PM5;PP1,PP2;BP1;PP5,PS4;PM1;PM2;PM5;PM6;PP1;PP3;BP2,0.292257785797119,PM5;PP3;PP1;PM2;PM1;PS4,PM6;BP2,,"The c.2167C>G (p.Arg723Gly) variant in MYH7 has been reported in 12 individuals with hypertrophic cardiomyopathy (PS4; PMID:11113006; PMID:19150014; PMID:17097032; Partners LMM ClinVar SCV000059422.5; SHaRe consortium, PMID: 30297972). This variant segregated with disease in >20 affected individuals (PP1_Strong; PMID:11113006). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2167C>T p.Arg723Cys - ClinVar Variation ID 14095). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_ Strong; PM1; PM2; PM5; PP3",,, +NM_000257.3(MYH7):c.2156G>A,PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5,7.87559461593628,PM1;PM5,,PM2;PP3,PM1;PM2;PP2;PP3;PP5;BP1,0.430699110031128,PM1;PM2;PP3,PS4;PM5;PP1,PP2;BP1;PP5,PS4;PM1;PM2;PM5;PP1;PP3,0.335282564163208,PM5;PP3;PP1;PM2;PM1;PS4,,,"The c.2156G>A (p.Arg719Gln) variant in MYH7 has been reported in >30 individuals with hypertrophic cardiomyopathy (PS4; PMID:7848441; PMID:16199542; PMID:15358028; PMID:18411228; Partners LMM ClinVar SCV000059421.5; AGCMC Sydney ClinVar SCV000212634.1; SHaRe consortium, PMID: 30297972). This variant segregated with disease in 7 affected individuals (PP1_Strong; PMID:7848441; Partners LMM ClinVar SCV000059421.5). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.2155C>T p.Arg719Trp ClinVar Variation ID 14104). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_ Strong; PM1; PM2; PM5; PP3",,, +NM_000257.3(MYH7):c.1208G>A,PS3;PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5,1472.01292085648,PP3;PM1;PM5,,PM2;PP1,PM1;PM2;PP2;PP3;PP5;BP1,0.392212629318237,PM1;PM2;PP3,PS4;PM5;PP1;PS3,PP2;BP1;PP5,PS4;PM1;PM2;PM5;PP1;PP3,0.335064649581909,PM5;PP3;PP1;PM2;PM1;PS4,,PS3,"The c.1208G>A (p.Arg403Gln) variant in MYH7 has been reported in >30 individuals with hypertrophic cardiomyopathy and segregated with disease in >30 affected family members (PS4 and PP1_Strong; PMID:1638703; PMID:1975517; PMID:7789380; PMID:12975413; PMID:24268868; PMID:10725281; PMID:20800588; PMID:12707239; PMID:27532257; AGCMC Sydney ClinVar SCV000692503.1; Invitae ClinVar SCV000253815.4; Partners LMM ClinVar SCV000059359.5; SHaRe consortium, PMID: 30297972). Mouse model indicates that this variant disrupts the function of MYH7 and leads to a phenotype consistent with HCM (PS3: PMID:8614836). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.1207C>T (p.Arg403Trp) - Variation ID 14102). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS3; PS4; PP1_ Strong; PM1; PM2; PM5; PP3",,, +NM_000257.3(MYH7):c.1207C>T,PS4;PM1;PM2;PM5;PP1;PP3,PM1;PM5;PP3;BP4,7.6662495136261,PP3;PM1;PM5;PM2,BP4,PP1,PM1;PM2;PP2;PP5;BP1,0.383901357650757,PM2;PM1,PS4;PM5;PP1;PP3,PP2;BP1;PP5,PS3;PS4;PM1;PM2;PM5;PP1;PP3,0.299535274505615,PM5;PP3;PP1;PM2;PM1;PS4,PS3,,"The c.1207C>T (p.Arg403Trp) variant in MYH7 has been reported in >20 individuals with hypertrophic cardiomyopathy and segregated with disease in >20 affected family members (PS4 and PP1_Strong; PMID:1052196; PMID:7662452; PMID:7848420; PMID:8254035; PMID:8268932; PMID:12707239; PMID:12974739; PMID:15010274; PMID:15856146; PMID:17612745; PMID:20428263; PMID:21239446; PMID:26383716; Partners LMM ClinVar SCV000059358.5; AGCMC Sydney ClinVar SCV000212643.1; SHaRe consortium, PMID: 30297972). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.1208G>A p.Arg403Gln - Variation ID 14087). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_Strong; PM1; PM2; PM5; PP3",,, +NM_000257.3(MYH7):c.1358G>A,PS4;PM1;PM2;PM5;PM6;PP3,PM1;PM5,7.4386739730835,PM1;PM5;PM2,,PS4;PP3,PM1;PM2;PP2;PP3;PP5;BP1,0.402814388275147,PM1;PM2;PP3,PS4;PM5;PM6,PP2;BP1;PP5,PS4;PM1;PM2;PM5;PP1;PP3,0.315271615982056,PM5;PP3;PM2;PM1;PS4,PP1,PM6,"The c.1358G>A (p.Arg453His) variant in MYH7 has been reported in >12 individuals with hypertrophic cardiomyopathy (PS4; PMID:27532257; PMID:20428263; PMID:15858117; PMID:20800588; PMID:21835320; PMID:22429680; Partners LMM ClinVar SCV000059369.5; Invitae ClinVar SCV000253816.4; SHaRe consortium, PMID: 30297972). This variant was been identified as a de novo occurrence in 1 proband with hypertrophic cardiomyopathy (PM6; PMID:20428263). This variant was absent from large population studies (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; c.1357C>T p.Arg453Cys; ClinVar Variation ID 14089). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PM1; PM2; PM5; PM6; PP3",,, +NM_002880.3(RAF1):c.775T>A,PS3;PS4;PM1;PM2;PM5;PM6;PP1;PP2;PP3,PM1;PM5,8.5560519695282,PP2;PP3;PM1;PM5,,PM2;PS3;PS4,PM1;PM2;PP3;PP5,0.374517202377319,PM1;PM2;PP3,PP2;PP1;PS3;PS4;PM5;PM6,PP5,PS4;PM1;PM2;PM5;PM6;PP3,0.330689191818237,PM6;PM5;PP3;PM2;PM1;PS4,,PP2;PP1;PS3,"The c.775T>A (p.Ser259Thr) variant in RAF1 has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; APHP-Robert Debré Hospital internal data; GTR ID's: 28338). The p.Ser259Thr variant has been identified in at least 8 independent occurrences in patients with a RASopathy (PS4_Supporting; GeneDx, Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 21766, 506381 PMID: 21784453; ClinVar SCV000061360.5; SCV000209017.10). The p.Ser259Thr variant in RAF1 has been reported to segregate with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 506381; ClinVar SCV000209017.9). In vitro functional studies provide some evidence that the p.Ser259Thr variant may impact protein function (PS3; PMID: 21784453, 20052757). At least 2 other pathogenic missense variants have been previously identified at this codon of RAF1 which may indicate that this residue is critical to the function of the protein (PM5_Strong; ClinVar 40603, 40602, 228288). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of RAF1 (PM1; PMID 29493581). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ser259Thr variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6_Strong, PS4_Supporting, PP1, PM5_Strong, PM2, PM1, PP2, PP3, PS3.",,, +NM_004985.4(KRAS):c.101C>T,PS2;PM2;PM5;PP2;PP3,PM5;PP3;BP4,16.2139370441437,PP2;PM5;PP3;PM2,BP4,PS2,PM1;PM2;PP3;PP5,0.396968364715576,PM2;PP3,PP2;PM5;PS2,PP5;PM1,PS3;PS4;PM1;PM2;PM5;PM6;PP1;PP2;PP3,0.283566236495972,PP3;PP2;PM5;PM2,PM6;PS3;PP1;PM1;PS4,PS2,"The c.101C>T (p.Pro34Leu) variant in KRAS has been reported as a confirmed de novo occurrence in a patient with clinical features of a RASopathy (PS2; PMID 17056636, 20949621). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). A different pathogenic missense variant has been previously identified at this codon of KRAS which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 12590). Computational prediction tools and conservation analysis suggest that the p.Pro34Leu variant may impact the protein (PP3; PMID: 24803665). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PS2, PM2, PM5, PP3, PP2.",,, +NM_002755.3(MAP2K1):c.388T>C,PS4;PM2;PM5;PM6;PP2;PP3,PM1;PM5;PP3;BP4,2686.98474836349,PM5;PP3,PM1;BP4,PP2;PM2,PM1;PM2;PP2;PP3;PP5,0.485947132110596,PP2;PM2;PP3,PS4;PM5;PM6,PP5;PM1,PS2;PM2;PM5;PP2;PP3,0.37100625038147,PP3;PP2;PM5;PM2,PS2,PM6;PS4,"The c.388T>C (p.Tyr130His) variant in MAP2K1 has been reported as an unconfirmed de novo occurrence in two probands with clinical features of a RASopathy (PM6_Strong; PMID: 1915617, Ambry Genetics internal data, ClinVar SCV000740998.1). One of these patients had a clinical diagnosis of cardiofaciocutaneous syndrome (PS4_Supporting). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The variant is located in the MAP2K1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). The variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K1 (PM1 not applied; PMID 29493581). Moreover, a different pathogenic missense variant has been previously identified at this codon of MAP2K1 which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 13351). Computational prediction tools and conservation analysis suggest that the p.Tyr130His variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM6_Strong, PM5, PM2, PP2, PP3.",,, +NM_000540.3(RYR1):c.1840C>T,PS3;PS4;PM5;PP1;PP3;BS2,,0.976229429244995,PM5;PP3,,PP1;BS2,PM1;PM2;PP3,0.397022247314453,PP3,PP1;PS3;PS4;PM5;BS2,PM2;PM1,PS4;PM2;PM5;PM6;PP2;PP3,0.328364372253418,PP3;PS4;PM5,PP2;PM6;PM2,PP1;PS3;BS2,"This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions.This sequence variant predicts a substitution of Arginine with Cysteine at codon 614 of the RYR1 protein, p.(Arg614Cys). The maximum allele frequency for this variant among the six major gnomAD populations is NFE: 0.00019, a frequency consistent with pathogenicity for MHS. This variant has been reported in over 100 unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, over 100 of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (if the proband was unavailable for testing, a positive diagnostic test result in a mutation-positive relative was counted), PS4 (PMID:24433488, PMID:16163667, PMID:30236257, and others). This variant has been identified in an individual with negative IVCT/CHCT results, BS2_Moderate (PMID:10484775). Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:26115329). This variant does not reside in a hotspot for pathogenic variants that contribute to MHS (PMID: 21118704). Another variant that has been assessed as pathogenic occurs at this codon, p.(Arg614Leu), PM5 (PMID:16917943). p.(Arg614Cys) segregates with MHS in 38 individuals PP1_Strong, (PMID:25960145, PMID:7586638, PMID:11493496 and others). A REVEL score >0.85 supports a pathogenic status for this variant, PP3_Moderate. Criteria implemented: PS3_Moderate, PS4, PM5, PP1_Strong, PP3_Moderate, BS2_Moderate. Based on using Bayes to combine criteria this variant is assessed as Pathogenic, (PMID: 29300386).",,, +NM_000540.3(RYR1):c.6487C>T,PS3;PS4;PM1;PM5;PP1;PP3;BS2,,0.903173446655273,PM1;PM5;BS2,,PS3;PS4;PP3,PM1;PM2;PP3,0.413597583770752,PM1;PP3,PP1;PS3;PS4;PM5;BS2,PM2,PS3;PS4;PM5;PP1;PP3;BS2,0.315521240234375,PM5;PP3;PS3;BS2;PP1;PS4,,PM1,"This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions.This sequence variant predicts a substitution of Arginine with Cysteine at codon 2163 of the RYR1 protein, p.(Arg2163Cys). The maximum allele frequency for this variant among the six major gnomAD populations is SAS: 0.000033, a frequency consistent with pathogenicity for MHS. This variant has been reported in three unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, three of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (if the proband was unavailable for testing, a positive diagnostic test result in a mutation-positive relative was counted), PS4_Moderate (PMID:10484775, PMID:30236257, PMID:9497245). This variant has been identified in an individual with a negative IVCT/CHCT result, BS2_Moderate. Functional studies in HEK293 cells show an increased sensitivity to RYR1 agonists, PS3_Moderate (PMID:9873004). Another variant has been assessed as pathogenic at this codon, p.(Arg2163His), PM5 (PMID:30236257 ). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, use PM1_Supporting to avoid overweighting with PM5 (PMID: 21118704). This variant segregates with MHS in over 15 individuals PP1_Strong, (PMID:9497245, PMID:30236257, PMID:10484775). A REVEL score >0.85 supports a pathogenic status for this variant, PP3_Moderate. Based on using Bayes to combine criteria this variant is assessed as Pathogenic, (PMID: 29300386). Criteria implemented: PS3_Moderate, PS4_Moderate, PM1_Supporting, PM5, PP1_Strong, PP3_Moderate, BS2_Moderate.",,, +NM_003159.2(CDKL5):c.215T>C,PS3;PS4;PM2;PM5;PM6;PP3,,0.900096416473389,PP3,,PM5;PM2,PM1;PM2;PP2;PP3;PP5,0.433248281478882,PM2;PP3,PS4;PM5;PM6;PS3,PP2;PP5;PM1,PS3;PS4;PM1;PM5;PP1;PP3;BS2,0.328516960144043,PP3;PS3;PS4;PM5,PP1;PM1;BS2,PM6;PM2,"The p.Ile72Thr variant in CDKL5 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with CDKL5 disease (PMID 19396824, 19241098) (PM6). The p.Ile72Thr variant in CDKL5 has been reported in at least 3 other individuals with CDKL5 disease (PMID 19396824, 19241098, 25657822, ClinVar) (PS4_moderate). The p.Ile72Thr variant in CDKL5 is absent from gnomAD (PM2). Multiple likely pathogenic missense variants have been previously identified within this codon (p.Ile72Asn; p.Ile72Met) which indicates that this residue is critical to the function of the protein (PMID 28074849, 27779742, 16015284) (PM5_strong). Phosphoproteomic screening of the cellular substrates of CDKL5 (MAP1S, CEP131 and DLG5) has shown that the p.Ile72Thr variant impacts protein function (PMID 30266825) (PS3_supporting). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own(PP3). In summary, the p.Ile72Thr variant in CDKL5 is classified as Pathogenic for CDKL5 disease based on the ACMG/AMP criteria (PM5_strong, PM6, PS4_moderate, PS3_supporting, PM2_supporting, PP3).",,, +NM_001323289.1:c.59G>T,PS2;PM1;PM2;PM5;PP3,PM1;PM5;PP3;BP4,7.76839661598206,PM1;PM5;PP3,BP4,PM2,PM1;PM2;PM5;PP2;PP3,0.394157886505127,PP3;PM1;PM2;PM5,PS2,PP2,PS3;PS4;PM2;PM5;PM6;PP3,0.366951942443848,PP3;PM5;PM2,PM6;PS4;PS3,PS2;PM1,"The p.Gly20Val variant in CDKL5 occurs in the de novo state (biological parentage confirmed) in this individual (PS2). Multiple pathogenic missense variants have been previously identified within this codon which indicates that this residue is critical to the function of the protein (PMID 23064044, 20397747) (PM5_Strong). The p.Gly20Val variant in CDKL5 is absent from gnomAD (PM2_Supporting). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own (PP3). In summary, the p.Gly20Val variant in CDKL5 is classified as pathogenic for CDKL5-associated disorder based on the ACMG/AMP criteria (PS2, PM5_strong, PM2_supporting, PP3).",,, +NM_014297.5(ETHE1):c.488G>A,PS3;PM3;PM5;PP3;PP4,PM1;PM2;PM5;PP3;BP4,131.541824579239,PM5;PP3,PM1;BP4;PM2,PM3,PM1;PM2;PP3;PP5,0.372634172439575,PP3,PM5;PS3;PM3;PP4,PM1;PM2;PP5,PS2;PM1;PM2;PM5;PP3,0.338687181472778,PP3;PM5,PS2;PM1;PM2,PM3;PP4;PS3,"The c.488G>A (NM_014297.5) variant in ETHE1 is a missense variant predicted to cause substitution of arginine by glutamine at amino acid 163 (p.R163Q). The highest population minor allele frequency for this variant in gnomAD v2.1.1 is 0.00005 (13/251,458 alleles) in the general population, which is higher than the ClinGen ETHE1 threshold < 0.00002 for PM2, thus it does not meet this criterion. This variant was originally reported in two compound heterozygous (c.131_132delAG; p. E44fsX105) relatives who both had developmental delay, petechiae, orthostatic acrocyanosis, chronic diarrhea, and ethylmalonic aciduria which is a phenotype highly specific to ethylmalonic encephalopathy (PP4_moderate; PMID: 14732903). This variant has been detected in at least 9 patients reported in the literature with ethylmalonic encephalopathy, however, many of the cases are not scoreable according to the SVI recommendation for in trans criterion for PM3, as parental phasing was not performed or the second variant was a VUS (PMID: 18593870; PMID: 16183799, PMID: 30298498). After review of scoreable cases, it was determined by the ETHE1 VCEP that four reported cases were scorable. A single relative from family L from PMID: 14732903 was awarded 1.0 as this patient was a compound heterozygote for an upstream truncating variant (c.131_132delAG; p. E44fsX105), which was confirmed in trans by segregation analysis. Additionally, while the p.E44fsX105 has not been formally curated at this time, given that the p.E44fsX105 is a truncating variant that is predicted to undergo nonsense mediated decay, it is also a strong candidate for a pathogenic classification; the VCEP agreed that this was justification to score this case as 1.0. Patients reported in PMID: 22020834 and PMID: 27771676 were each awarded 0.25 for their respective VUS’s, which were also confirmed in trans. A homozygous patient reported in PMID: 27391121 in whom homozygosity was confirmed via trio WES including parental samples was scored 0.5. This was confirmed by Baylor Genetics who performed the testing for this study (PM3_Strong; Total score- 2.0). ETHE1 encodes persulfide dioxygenase. Persulfide dioxygenase activity measured in recombinant human ETHE1 proteins (both wild-type and p.R163Q) expressed in E.Coli (purified to homogeneity) showed that the p.R163Q recombinant E.Coli only exhibited ~10% of wild-type catalytic activity, indicating that this variant impacts protein function (PS3_supporting; PMID: 25198162). One other missense variant [c.487C>T, p.R163W; PMID 14732903, PMID 16828325, PMID 16183799, PMID 28698729; ClinVar Variation ID: 2317], in the same codon has been classified as pathogenic for ethylmalonic encephalopathy by the ClinGen ETHE1 VCEP (PM5). The computational predictor [REVEL] gives a score of 0.928, which is above the threshold of 0.75, evidence that correlates with impact on ETHE1 function (PP3). In summary, this variant meets the criteria to be classified as pathogenic for Autosomal Recessive Ethylmalonic Encephalopathy. ACMG/AMP criteria applied, as specified by the ClinGen ETHE1 VCEP (version 1.0): PM3_strong, PP4_Moderate, PS3_supporting, PM5, PP3. Approved 7/12/2021.",,, +NM_000257.4(MYH7):c.2710C>T,PS4;PM2;PM5;PM6;PP1;PP3,PM1;PM2;PM5,7.78034257888794,PM5;PP3;PM2,PM1,PP1;PS4,PS3;PM1;PM2;PP2;PP3;BP1,0.371264696121216,PP3;PM2,PM6;PS4;PP1;PM5,PS3;PM1;PP2;BP1,PS3;PM3;PM5;PP3;PP4,0.336124420166016,PP3;PM5,PM3;PP4;PS3,PP1;PM6;PS4;PM2,"The NM_000257.4:c.2710C>T (p.Arg904Cys) variant in MYH7 has been identified in 4 individuals with DCM in the literature (1 of whom also had LVNC; van Spaendonck-Zwarts 2013 PMID:23349452; van der Zwaag 2011 PMID:20573160; Walsh 2017 PMID:27532257; Miller 2017 PMID29212898) and 3 individuals with LVNC (2 of which were pediatric; Yang 2014 PMID:25326635; Wang 2017 PMID:28855170; van Waning 2018 PMID:29447731). This variant was identified in 8 individuals with DCM and 1 proband with LVNC by clinical laboratories (GeneDx pers. comm.; Invitae pers. comm.; LMM pers. comm.; OMGL pers comm.). Only probands with DCM are counted towards PS4 (n=12; PS4_Moderate). This variant segregated with DCM in 15 affected individuals from 4 families (PP1_Strong; van der Zwaag 2011 PMID:20573160; GeneDx pers. comm.; LMM pers. comm.; OMGL pers. comm.) and was assumed de novo in 1 of the above cases (PM6; GeneDx pers. comm.). This variant has been identified in 0.010% (1/10080) of Ashkenazi Jewish chromosomes by gnomAD v2.1.1 (https://gnomad.broadinstitute.org), but was absent from all other populations. A different pathogenic missense variant has been previously identified at this codon, which indicates that this residue may be critical to the function of the protein (PM5; c.2711G>A p.Arg904His - Variation ID 42926). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for dilated cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (Kelly 2018 PMID:29300372): PS4_Moderate, PP1_Strong, PM6, PM2, PM5, PP3.",,, +NM_004958.4(MTOR):c.4448G>A,PS2;PS4;PM1;PM2;PM5;PP2,PM1;PM5;PP3;BP4,13.0135538578033,PP2;PM1;PM5,BP4;PP3,PM2;PS2,PM1;PM2;PP3;PP5,0.388700723648071,PM1;PM2,PS4;PP2;PS2;PM5,PP3;PP5,PS4;PM2;PM5;PM6;PP1;PP3,0.321320533752441,PS4;PM5;PM2,PP3;PP1;PM6,PP2;PM1;PS2,"The c.4448G>A (NM_004958.4) variant in MTOR is a missense variant predicted to cause substitution of (p.Cys1483Tyr). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). MTOR, in which the variant was identified, is defined by the ClinGen Brain Malformations Expert Panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). A different amino acid change (p.Cys1483Arg), at this locus is classified as pathogenic for Overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes by the ClinGen BMEP (PM5). This variant resides within the kinase domain of MTOR that is defined as a critical functional domain by the ClinGen BMEP (PMIDs: 23322780, 27482884, 21210909) (PM1_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4; PMIDs: 22729223; 28892148; 25599672; 26619011; identified in 2 individuals with neuroimaging demonstrating at least one large cerebral hemisphere with cortical malformation(s), 1 individual with macrocephaly ( >=2 SD) and Developmental Delay or Intellectual disability without cortical malformations, it has been shown to demonstrate an increase cell growth phenotype in patient cell lines and at least 3 tumor samples in the literature and COSMIC). This variant has been confirmed de novo and has been identified with variable allelic fractions consistent with a post-zygotic event (PS2_Strong; PMID: 28892148). In summary, this variant meets the criteria to be classified as Pathogenic for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: PM2_P, PP2, PM5, PM1_P, PS4, PS2; 13 points(VCEP specifications version 1; Approved: 1/31/2021)",,, +NM_004958.3:c.5930C>G,PS2;PS3;PS4;PM1;PM2;PM5;PP2,,4.40990972518921,PM1;PM5,,PP2;PM2;PS3,PM1;PM2;PM5;PP3,0.407511234283447,PM1;PM2;PM5,PS3;PP2;PS2;PS4,PP3,PS2;PS4;PM1;PM2;PM5;PP2,0.321476936340332,PM5;PP2;PM2;PS2;PM1;PS4,,PS3,"The c.5930C>G (NM_004958.4) variant in MTOR is a missense variant predicted to cause substitution of (p.Thr1977Arg). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). MTOR, in which the variant was identified, is defined by the ClinGen Brain Malformations Expert Panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). A different amino acid change (p.Thr1977Lys), at this locus is classified as pathogenic for Overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes by the ClinGen BMEP (PM5). This variant resides within the kinase domain of MTOR that is defined as a critical functional domain by the ClinGen BMEP (PMIDs: 23322780, 27482884, 21210909) (PM1_Supporting). This variant has been shown to significantly increase phosphorylation levels in experiments with case and controls cells of similar isogenic backgrounds indicating that this variant impacts protein function (PMID: 24631838) (PS3_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_M; PMIDs: 25799227, 29281825, identified in 2 individuals with neuropathology confirmatory of a malformation of cortical development, 1 individual with neuroimaging appearance consistent with a malformation of cortical development (without neuropathology), 5 tumor samples in the literature and COSMIC). Testing of unaffected and affected tissue show variable allelic fractions consistent with a post-zygotic event (PS2_Moderate; PMID: 25799227). In summary, this variant meets the criteria to be classified as Pathogenic for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: PM2_P, PP2, PM5, PM1_P, PS3_P, PS4_M, PS2_M; 10 points (VCEP specifications version 1; Approved: 1/31/2021)",,, +NM_002880.3(RAF1):c.769T>C,PS4;PM2;PM6;PP2,,0.712877035140991,PM2,,PP2;PM6,PM1;PM2;PP3;PP5,0.365538358688354,PM2,PM6;PS4;PP2,PP3;PP5;PM1,PS2;PS3;PS4;PM1;PM2;PM5;PP2,0.328930139541626,PP2;PS4;PM2,PS2;PM1;PS3;PM5,PM6,"The c.769T>C (p.Ser257Pro) variant in RAF1 was absent from large population studies (PM2; gnomAD.broadinstitute.org). It has been identified in 3 patients with clinical features of a RASopathy (PS4_Moderate, SCV000206160.5; SCV000209015.10; PMID 23321623). In one proband the variant occurred de novo without parental confirmation (PM6). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 13957) Furthermore, the p.Ser257Pro variant is located in RAF1, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM1, PM2, PM6, PP2.",,, +NM_005343.3(HRAS):c.175G>A,PS4;PM1;PM2;PP1;PP2;PP3,,0.676827907562256,PP2;PM1;PP3,,PM2;PP1,PM1;PM2;PP3;PP5,0.399978876113892,PP3;PM2;PM1,PS4;PP2;PP1,PP5,PS4;PM2;PM6;PP2,0.329801321029663,PP2;PS4;PM2,PM6,PP3;PP1;PM1,"The c.175G>A (p.Ala59Thr) variant in HRAS has been identified in at least 3 independent occurrences in patients with a RASopathy (PS4_Moderate; GeneDx, Partners LMM, Invitae internal data; ClinVar SCV000198374, SCV000950586). The p.Ala59Thr variant segregated with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Partners LMM internal data). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of HRAS (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ala59Thr variant may impact the protein (PP3). The variant is located in the HRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM1, PM2, PS4_Moderate, PP1, PP2, PP3.",,, +NM_005633.3(SOS1):c.1018C>T,PP2;BS1;BS4;BP5,,0.686291694641113,PP2,,BS4;BS1,PM1;PM2;PP3;BP6;BS2,0.363005638122559,,BS4;BP5;PP2;BS1,PM1;BS2;BP6;PP3;PM2,PS4;PM1;PM2;PP1;PP2;PP3,0.335641622543335,PP2,PP3;PP1;PM2;PM1;PS4,BS1;BP5;BS4,"The c.1018C>T (p.Pro340Ser) variant in the SOS1 gene has been found not to segregate in a family member of a patient who underwent testing for RASopathies as well as another adult who was unaffected (BS4; GeneDx, Invitae internal data; GTR Lab ID: 26957, 500031; SCV000514724.5, SCV000659124.2). This variant has also been identified in a patient with an alternate molecular basis of disease (BP5; PMID 22585553). The filtering allele frequency of the p.Pro340Ser variant is 0.022% for East Asian exomes in the gnomAD database (20/251276 with 95% CI), which is high enough frequency to be considered strong evidence for the variant being benign by the ClinGen RASopathy Expert Panel (BS1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BS4, BP5, BS1.",,, +NM_002880.3(RAF1):c.94A>G,PP2;BS1;BS2;BP4;BP5,,0.663318634033203,BS1;BS2,,PP2;BP4,PM1;BP6,0.355585336685181,,BP4;BS2;PP2;BS1;BP5,PM1;BP6,PP2;BS1;BS4;BP5,0.307804107666016,PP2;BS1;BP5,BS4,BP4;BS2,"The c.94A>G (p.Ile32Val) variant in the RAF1 gene has been identified in patients who underwent testing for a RASopathy, however it has also been identified in multiple adults who did not have clinical features of a RASopathy (BS2, BP5; Invitae, EGL Diagnostics, GeneDx internal data; GTR Lab ID: 500031, 500060; SCV000287747.4, SCV000227277.5, SCV000209002.14). The filtering allele frequency of the p.Ile32Val variant is 0.017% for European (non-Finnish) genomes in the gnomAD database (8/31404 with 95% CI) which is a high enough frequency to be considered strong evidence that the variant is benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BS1). Computational prediction tools and conservation analysis suggest that the p.Ile32Val variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BS2, BP5, BS1, BP4.",,, +NM_000314.6(PTEN):c.520T>A,PS3;PM2;PP2,,0.683493375778198,PP2,,PM2,PM1;PM2;PP3;PP5;BP1,0.369442939758301,PM2,PS3;PP2,PP3;PM1;PP5;BP1,PP2;BS1;BS2;BP4;BP5,0.305303335189819,PP2,BS1;BP5;BP4;BS2,PS3;PM2,"PTEN c.520T>A (p.Tyr174Asn) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 10866302, PMID 29706350)PM2: Absent in large sequenced populations (PMID 27535533)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.",,, +NM_004333.4(BRAF):c.1595G>A,PS4;PM2;PM6;PP2;PP3,PM1;PP3;BP4,7.59744334220886,PP2;PP3,PM1;BP4,PM6;PM2,PM1;PM2;PP5,0.370512962341309,PM2,PS4;PP3;PM6;PP2,PP5;PM1,PS3;PM2;PP2,0.348472833633423,PP2;PM2,PS3,PP3;PM6;PS4,"The c.1595G>A (p.Cys532Tyr) variant in BRAF has been observed in three probands with RASopathies (PS4_Moderate; Laboratory for Molecular Medicine, Hopital Universitaire Robert Debre internal data, ClinVar SCV000197143.4) It has also been seen as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; EGL internal data, ClinVar SCV000112809.8). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Cys532Tyr variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM2, PM6, PP2, PP3.",,, +NM_000314.6(PTEN):c.209T>C,PS3;PS4;PM2;PP2,PM1;PP3;BP4,12.6151711940765,PP2,PM1;BP4;PP3,PM2;PS4,PM1;PM2;PP3;PP5;BP1,0.378013134002686,PM2,PS3;PS4;PP2,PP5;PP3;PM1;BP1,PS4;PM2;PM6;PP2;PP3,0.304322481155395,PP2;PS4;PM2,PP3;PM6,PS3,PTEN c.209T>C (p.Leu70Pro) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 29706350)PM2: Absent in large sequenced populations (PMID 27535533).PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.PS4_P: Proband(s) with phenotype specificity score of 1-1.5. (internal laboratory contributor(s) ClinVar Organization ID: 26957),,, +NM_000314.6(PTEN):c.170T>G,PS3;PM2;PP2,,3.60957360267639,PM2,,PP2,PM1;PM2;PP3;PP5;BP1,0.366116762161255,PM2,PS3;PP2,PP5;PP3;PM1;BP1,PS3;PS4;PM2;PP2,0.315280199050903,PP2;PS3;PM2,PS4,,"PTEN c.170T>G (p.Leu57Trp) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 9256433, 29706350)PM2: Absent in large sequenced populationsPP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.",,, +NM_000314.6(PTEN):c.331T>C,PS3;PS4;PM2;PP2,,0.682560920715332,,,PP2;PM2,PM1;PM2;PP3;PP5;BP1,0.355661869049072,PM2,PS3;PS4;PP2,PP5;PP3;PM1;BP1,PS3;PM2;PP2,0.324536323547363,PP2;PS3;PM2,,PS4,"PTEN c.331T>C (p.Trp111Arg) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 29785012, 29706350)PM2: Absent in large sequenced populations (PMID 27535533).PS4_M: Probands with phenotype specificity score of 2-3.5. (internal laboratory contributor(s) ClinVar Organization ID: 61756, ClinVar Organization ID: 19864)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.",,, +NM_000314.6(PTEN):c.181C>G,PS3;PM2;PM6;PP2,,0.658978223800659,PP2,,PM2;PS3,PM1;PM2;PP3;PP5;BP1,0.35837984085083,PM2,PS3;PM6;PP2,PP5;PP3;PM1;BP1,PS3;PS4;PM2;PP2,0.320051670074463,PP2;PS3;PM2,PS4,PM6,"PTEN c.181C>G (p.His61Asp) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 29706350, PMID 17942903, PMID 21828076)PM2: Absent in large sequenced populations (PMID 27535533).PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (PMID 11748304)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.",,, +NM_004333.4(BRAF):c.739T>G,PS4;PM1;PM2;PP2;PP3,,0.671882152557373,PP2;PM2,,PM1;PP3,PM1;PM2;PP3;PP5,0.352654218673706,PM2;PP3;PM1,PS4;PP2,PP5,PS3;PM2;PM6;PP2,0.312778472900391,PP2;PM2,PM6;PS3,PP3;PM1;PS4,"The c.739T>G (p.Phe247Val) variant in BRAF has been identified in at least 2 independent occurrences in patients with clinical features of a RASopathy (PS4_Supporting; Partners LMM, GeneDx internal data; GTR Lab IDs 21766, 26957; ClinVar SCV000061624.5, SCV000330320.6). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). A different pathogenic missense variant (p.Phe247Leu) has been previously identified at this codon of BRAF which may indicate that this residue is critical to the function of the protein (PM5 not usable due to PM1 application; ClinVar 180784, 55793). Computational prediction tools and conservation analysis suggest that the p.Phe247Val variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM2, PM1, PP2, PP3.",,, +NM_002834.4(PTPN11):c.167T>C,PS4;PM2;PM5;PP2;PP3,,0.59926438331604,PP2;PM2;PP3,,PM5;PS4,PM1;PM2;PP3;PP5,0.351351261138916,PM2;PP3,PP2;PS4;PM5,PP5;PM1,PS4;PM1;PM2;PP2;PP3,0.308184146881104,PP3;PP2;PS4;PM2,PM1,PM5,"The c.167T>C (p.Ile56Thr) variant in PTPN11 has been identified in 2 related patients with clinical features of a RASopathy (PS4_Supporting, PP1; Invitae internal data; GTR Lab ID 500031; ClinVar SCV000659038.1). A different pathogenic missense variant (p.Ile56Val) has been previously identified at this codon of PTPN11 which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 40485). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). The variant is located in the PTPN11 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ile56Thr variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PP1, PM2, PM5, PP2, PP3.",,, +NM_005633.3(SOS1):c.512T>C,PS4;PM2;PM5;PM6;PP2,,0.646196365356445,PP2;PM2,,PM6;PM5,PM1;PM2;PP3;PP5,0.347958564758301,PM2,PP2;PS4;PM6;PM5,PP5;PP3;PM1,PS4;PM2;PM5;PP2;PP3,0.303659200668335,PP2;PS4;PM5;PM2,PP3,PM6,"The c.512T>C (p.Val171Ala) variant in SOS1 has been reported as an unconfirmed de novo occurrence in a patient with clinical features of a Noonan spectrum disorder (PM6; Partners LMM internal data; GTR Lab ID: 21766; ClinVar SCV000062240.5). The p.Val171Ala variant has also been identified in another independent occurrences in patients with clinical features of a familial RASopathy (PS4_Supporting; PMID: 29402968). This variant was absent from large population studies (PM2; gnomAD, http://gnomAD.broadinstitute.org). A different pathogenic missense variant (p.Val171Gly) has been previously identified at this codon of SOS1 which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 40654). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6, PM5, PM2, PS4_Supporting, PP2.",,, +NM_000314.6(PTEN):c.737C>T,PS2;PS4;PM2;PP2,,0.816348791122437,PP2,,PM2;PS4,PM1;PM2;PP3;PP5;BP1,0.36238431930542,PM2,PS2;PS4;PP2,PP5;PP3;PM1;BP1,PS4;PM2;PM5;PM6;PP2,0.313472509384155,PP2;PS4;PM2,PM6;PM5,PS2,"PTEN c.737C>T (p.P246L) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS2_VS: At least two proven OR one proven plus two assumed de novo observations in a patient with the disease and no family history. (PMID 23934111, internal laboratory contributor(s) SCV000222227.10)PS4: Probands with phenotype specificity score of 4-15.5. (PMID 24375884, PMID 10076877, PMID 22261759, PMID 23934111, internal laboratory contributor(s) SCV000222227.10)PM2: Absent in large sequenced populations. (PMID 27535533).PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.",,, +NM_000314.6(PTEN):c.510T>A,PS3;PS4;PM2;PP1;PP2,,0.608964920043945,,,PP2;PM2,PM1;PM2;PP3;PP5;BP1,0.346567869186401,PM2,PP1;PS3;PS4;PP2,PP5;PP3;PM1;BP1,PS2;PS4;PM2;PP2,0.328437328338623,PP2;PS4;PM2,PS2,PP1;PS3,"PTEN c.510T>A (p.Ser170Arg) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 17942903, PMID 10866302, PMID 9256433, PMID 21828076PS4_M: Probands with phenotype specificity score of 2-3.5. (PMID 17526800, PMID 23335809, PMID 30528446)PM2: Absent in large sequenced populations (PMID 27535533)PP1: Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed. (PMID 17526800, PMID 9241266)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.",,, +NM_000314.6(PTEN):c.368A>G,PS3;PM1;PM2;PM6;PP2,PM1;PP3;BP4,7.65471768379211,PP2;PM1,BP4;PP3,PM6;PM2,PM1;PM2;PP3;PP5;BP1,0.388467788696289,PM2;PM1,PS3;PP2;PM6,BP1;PP3;PP5,PS3;PS4;PM2;PP1;PP2,0.304508686065674,PP2;PS3;PM2,PP1;PS4,PM1;PM6,"PTEN c.368A>G (p.His123Arg) meets criteria to be classified as pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PS3: Phosphatase activity <50% of wild type (PMID 29706350)PM1: Located at a residue within a catalytic motif as defined by the ClinGen PTEN Expert Panel.PM2: Absent in large sequenced populations PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (PMID 10234502)PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.",,, +NM_005633.3(SOS1):c.322G>A,PS2;PS3;PS4;PM2;PM6;PP2,PM1,7.9345805644989,PP2;PM2,PM1,PM6;PS4,PM1;PM2;PP3;PP5,0.346650123596191,PM2,PS3;PS2;PP2;PS4;PM6,PP3;PP5;PM1,PS3;PM1;PM2;PM6;PP2,0.319913387298584,PP2;PM6;PS3;PM2,PM1,PS2;PS4,"The c.322G>A (p.Glu108Lys) variant in SOS1 has been reported as confirmed and unconfirmed occurrences in patients with clinical features of a RASopathy (PM6 and PS2; GeneDx, Partners LMM, APHP-Robert Debré Hospital internal data GTR Lab ID: 26957, 21766, 28338; ClinVar SCV000209088.9, SCV000062224.5, SCV000659144.2). The p.Glu108Lys variant has been identified in several independent occurrences in patients with clinical features of a RASopathy (PS4_Moderate; GeneDx, Partners LMM, APHP-Robert Debré Hospital internal data GTR Lab ID: 26957, 21766, 28338; ClinVar SCV000209088.9, SCV000062224.5, SCV000659144.2; PMID: 17143282; 23487764). In vitro functional studies provide some evidence that the p.Glu108Lys variant may impact protein function (PS3; PMID: 17143282, 23487764). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2, PS3, PM6, PS4_Moderate, PM2, PP2.",,, +NM_007373.3(SHOC2):c.4A>G,PS2;PS3;PS4;PM2;PP2,,12.7059478759766,PM2,,PP2;PS3,PM1;PP5,0.373383522033691,,PM2;PS3;PS2;PP2;PS4,PP5;PM1,PS2;PS3;PS4;PM2;PM6;PP2,0.325639963150024,PS3;PP2;PM2;PS2;PS4,PM6,,"The c.4A>G (p.Ser2Gly) variant in SHOC2 has been reported as a confirmed de novo occurrence in multiple patients with clinical features of a RASopathy (PS2_VeryStrong; Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg, APHP-Robert Debré Hospital internal data; GTR ID's: 21766, 506381, 28338; ClinVar SCV000062456.5, SCV000209051.10, SCV000263045.1 PMID 19684605, 21548061, 23918763, 22528146). The p.Ser2Gly variant has been identified in at least 5 independent occurrences in patients with clinical features of a RASopathy (PS4; Institute of Human Genetics, Otto von Guericke University Magdeburg, APHP-Robert Debré Hospital internal data GTR ID's: 506381, 28338; PMID: 25563136, 24458587). In vitro functional studies provide some evidence that the p.Ser2Gly variant may impact protein function (PS3; PMID: 19684605). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the SHOC2 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PS3, PS4, PM2, PP2.",,, +NM_002880.3(RAF1):c.775T>A,PS3;PS4;PM1;PM2;PM5;PM6;PP1;PP2;PP3,PM1;PM5,7.59474468231201,PP3;PM1;PM5;PM2,,PP2;PS3;PS4,PM1;PM2;PP3;PP5,0.350970983505249,PM2;PP3;PM1,PS3;PM5;PP2;PS4;PP1;PM6,PP5,PS2;PS3;PS4;PM2;PP2,0.361127614974976,PP2;PS4;PS3;PM2,PS2,PM6;PM5;PP3;PP1;PM1,"The c.775T>A (p.Ser259Thr) variant in RAF1 has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; APHP-Robert Debré Hospital internal data; GTR ID's: 28338). The p.Ser259Thr variant has been identified in at least 8 independent occurrences in patients with a RASopathy (PS4_Supporting; GeneDx, Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 21766, 506381 PMID: 21784453; ClinVar SCV000061360.5; SCV000209017.10). The p.Ser259Thr variant in RAF1 has been reported to segregate with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 506381; ClinVar SCV000209017.9). In vitro functional studies provide some evidence that the p.Ser259Thr variant may impact protein function (PS3; PMID: 21784453, 20052757). At least 2 other pathogenic missense variants have been previously identified at this codon of RAF1 which may indicate that this residue is critical to the function of the protein (PM5_Strong; ClinVar 40603, 40602, 228288). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of RAF1 (PM1; PMID 29493581). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ser259Thr variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6_Strong, PS4_Supporting, PP1, PM5_Strong, PM2, PM1, PP2, PP3, PS3.",,, +NM_002880.3(RAF1):c.1082G>C,PS4;PM2;PM6;PP2;PP3,PM1;PP3;BP4,13.5859696865082,PP2;PP3,PM1;BP4,PM6;PM2,PM1;PM2;PP3;PP5,0.416451215744019,PM2;PP3,PS4;PP2;PM6,PP5;PM1,PS3;PS4;PM1;PM2;PM5;PM6;PP1;PP2;PP3,0.336107730865479,PM6;PP3;PP2;PM2;PS4,PP1;PS3;PM1;PM5,,"The c.1082G>C (p.Gly361Ala) variant in RAF1 has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 506381 ClinVar SCV000209024.9). The p.Gly361Ala variant has been identified in at least 4 independent occurrences in patients with a RASopathy (PS4_Moderate; GeneDx, Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 21766, 506381; SCV000209024.9, SCV000061333.5). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Gly361Ala variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6_Strong, PS4_Moderate, PM2, PP2, PP3.",,, +NM_030662.3(MAP2K2):c.619G>A,PS2;PS4;PM2;PM6;PP2,,3.84742999076843,PM2,,PP2;PM6,PM1;PM2;PP5,0.393253087997437,PM2,PS4;PS2;PP2;PM6,PP5;PM1,PS4;PM2;PM6;PP2;PP3,0.326448202133179,PP2;PM6;PS4;PM2,PP3,PS2,"The c.619G>A (p.Glu207Lys) variant in MAP2K2 was absent from large population studies (PM2; gnomAD.broadinstitute.org). It has been identified in 6 individuals with clinical features of a RASopathy (PS4; SCV000204213.4, SCV000207959.10, SCV000815593.1, Otto von Guericke University Magdeburg internal data). One of these cases was a confirmed de novo occurrence and another was an unconfirmed de novo occurrence (PS2; PM6; SCV000815593.1, Otto von Guericke University Magdeburg internal data). Additionally, the c.619G>A (p.Glu207Lys) is located in MAP2K2, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4, PS2, PM6, PM2, PP2.",,, +NM_004985.4(KRAS):c.15A>T,PS4;PM2;PM6;PP2;PP3,,0.822210550308228,PP2;PP3,,PM2;PS4,PM1;PM2;PP3;PP5,0.357481002807617,PM2;PP3,PS4;PP2;PM6,PP5;PM1,PS2;PS4;PM2;PM6;PP2,0.316963195800781,PP2;PM6;PS4;PM2,PS2,PP3,"The c.15A>T (p.Lys5Asn) variant in KRAS has been reported in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID: 17056636, GeneDx internal data). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The p.Lys5Asn variant has been identified in at least 4 independent occurrences in patients with a RASopathy (PS4_Moderate; PMID: 17056636, GeneDx, EGL Genetics internal data, ClinVar SCV000202928.7). Computational prediction tools and conservation analysis suggest that the p.Lys5Asn variant may impact protein function (PP3). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM6_Strong, PM2, PP2, PP3.",,, +NM_000038.6(APC):c.295C>T,BS1;BS2;BP1;BP2;BP5,,0.765900611877441,BP1;BS1,,BP2;BS2,PM1;PM2;PP3;BP1,0.42238974571228,BP1,BS2;BP5;BS1;BP2,PM2;PP3;PM1,PS4;PM2;PM6;PP2;PP3,0.336857080459595,,PM6;PP3;PP2;PM2;PS4,BP2;BP5;BS2;BS1;BP1,"The c.295C>T variant in APC is a missense variant predicted to cause substitution of Arginine by Tryptophan at amino acid position 99 (p.Arg99Trp). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). The highest population minor allele frequency of the variant c.295C>T in gnomAD v2.1.1 (non-cancer) is 0.0007355 (95/129170 alleles) in the European (non-Finnish) population, which is higher than the HCCP VCEP threshold (≥ 0.001%) for BS1 (BS1). This variant has been observed in heterozygous state in more than 1000 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Invitae and Ambry Genetics internal data). It has also been observed once in a homozygous state (Ambry Genetics internal data). This variant has been observed 4 times with other APC variants deemed (likely) pathogenic by the HCCP VCEP in individuals with FAP (BP2; PMIDs 23159591, 25604157, Bonn internal data). Finally, this variant has been observed in 6 patients with an alternate molecular basis for disease (BP5; Leiden University Medical Center internal data). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS1, BS2, BP1, BP2 (VCEP specifications version 1; date of approval 12/12/2022).",,, +NM_000038.6(APC):c.715G>C,BS1;BS2;BP1,,0.680522441864014,BS1;BS2,,BP1,PM1;PM2;BP1,0.395238637924194,BP1,BS2;BS1,PM2;PM1,BS1;BS2;BP1;BP2;BP5,0.329262495040893,BS1;BP1;BS2,BP2;BP5,,"The c.715G>C variant in APC is a missense variant predicted to cause substitution of alanine by proline at amino acid 239 (p.Ala239Pro). This variant has been observed in ≥ 35 heterozygous individuals with no features or family history of FAP, worth ≥ 10 healthy individual points (BS2; Ambry, Invitae internal data). The highest allele frequency of this variant in gnomAD v2.1.1 (non-cancer) is 0.0002269 in East Asian population, which is higher than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) threshold (≥ 0.00001) for BS1 (BS1). Finally, APC is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS1, BS2, BP1. (VCEP specifications version 1; date of approval 12/12/2022).",,, +NM_000038.6(APC):c.995G>A,BS1;BS2;BP1,,0.679151058197022,BP1;BS2,,BS1,PM1;PM2;PP3;BP1,0.359575510025024,BP1,BS2;BS1,PM2;PP3;PM1,BS1;BS2;BP1,0.326711177825928,BS1;BP1;BS2,,,"The c.995G>A variant in APC is a missense variant predicted to cause substitution of Arginine by Glutamine at amino acid 332 (p.Arg332Gln). This variant has been observed in heterozygous state in >100 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics, Invitae, GeneDX internal data). The allele frequency of the c.995G>A variant in APC is 0.02% for the African sub-population (5/23604 alleles) in the non-cancer dataset from gnomAD (v2.1.1), which is higher than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) threshold (≥ 0.001%) for BS1, and therefore meets BS1. APC is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS1, BS2 and BP1 (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.1240C>T,BA1;BS2;BP1;BP2,PM1;PM2;PP3;BP4,7.89687919616699,BS2,PM1;BP4;PP3;PM2,;BA1,PM1;PM2;BP1;BS2,0.37108302116394,BS2;BP1,BP2;BA1,PM2;PM1,BS1;BS2;BP1,0.326195478439331,BP1;BS2,BS1,BP2;BA1,"The c.1240C>T variant in APC is a missense variant predicted to cause the substitution of arginine by cysteine at amino acid 414 (p.Arg414Cys). This variant has been observed in heterozygous state in ≥ 1000 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Invitae, Ambry, and GeneDX internal data). It has been observed in trans with a variant classified as Pathogenic by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) in an individual with FAP (BP2). The highest allele frequency of this variant is 0.001835 in European (Finnish) population, which is higher than the HCCP VCEP threshold (≥ 0.001) for BA1. Finally, APC is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BA1, BS2, BP1 and BP2 (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.2476T>G,BA1;BP1,PM1;PM2,12.8551404476166,BP1,PM1;PM2,BA1,PM1;PM2;BP1;BS2,0.404324531555176,BP1,BA1,BS2;PM2;PM1,BA1;BS2;BP1;BP2,0.342089176177979,BP1;BA1,BP2;BS2,,"The c.2476T>G variant in APC is a missense variant predicted to cause a substitution of leucine by valine at amino acid position 826 (p.Leu826Val). The highest population minor allele frequency in gnomAD v2.1.1 is 0.1576% in the non-cancer African/African American population, which is higher than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation threshold (>0.1%) for BA1, and therefore meets this criterion (BA1). Additionally, APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel as a gene for which primarily truncating variants are known to cause disease (BP1). Multiple lines of computational evidence suggest no splicing impact. In summary, this variant meets the criteria to be classified as Benign for FAP. ACMG/AMP criteria applied, as specified by the ClinGen/InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel: BA1, BP1 (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.4399C>T,BS1;BS2;BS3;BP1;BP5,PM1;PM2,13.758514881134,BP1;BS2,PM1;PM2,BS1;BP5,PM1;PM2;BP1,0.780457496643066,BP1,BS3;BP5;BS1;BS2,PM2;PM1,BA1;BP1,0.324827671051025,BP1,BA1,BS1;BP5;BS3;BS2,"The c.4399C>T variant in APC is a missense variant predicted to cause the substitution of Proline by Serine at amino acid position 1467 (p.Pro1467Ser). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in a heterozygous state in 75 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics, Invitae and GeneDX internal data). In addition, it has also been observed in 1 patient with an alternate molecular basis for disease – a pathogenic MSH6 germline variant (BP5; Melbourne Internal data). Functional study of β-catenin-regulated transcription assays indicate that this alteration suppresses CRT as effectively as the wild type (BS3_Supporting; PMID: 18199528). The highest population minor allele frequency in gnomAD v2.1.1 (non-cancer) is 0.0048% in European (non-Finnish) population, which is higher than the HCCP VCEP threshold (≥ 0.001%) for BS1, and therefore meets this criterion (BS1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS1, BS2, BS3_Supporting, BP1 and BP5 (VCEP Specification version 1, date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.4420G>A,BA1;BS3;BP1,,3.18321204185486,BP1;BA1,,BS3,PM1;BP1;BP6;BS1;BS2,0.691692352294922,BP1,BS3;BA1,BS2;BS1;BP6;PM1,BS1;BS2;BS3;BP1;BP5,0.331009864807129,BS3;BP1,BS1;BP5;BS2,BA1,"The c.4420G>A variant in APC is a missense variant predicted to cause the substitution of Alanine by Threonine at amino acid position 1474 (p.Ala1474Thr). The highest population minor allele frequency of this variant in gnomAD v2.1.1 (non-cancer) is 1.13% in the African/African American population, which is higher than the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel’s (HCCP VCEP) threshold (≥ 0.1%) for BA1, and therefore meets this criterion (BA1). Functional study of β-catenin-regulated transcription assays indicate that this alteration suppresses CRT as effectively as wild type (BS3_Supporting; PMID: 18199528). Finally, APC is defined by the HCCP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BA1, BP1, BS3_Supporting (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.5465T>A,BA1;BP1,,0.794879198074341,BP1,,BA1,PM1;BA1;BP1;BP6;BS1;BS2,0.420234441757202,BA1;BP1,,BS2;BS1;BP6;PM1,BA1;BS3;BP1,0.312121868133545,BP1;BA1,BS3,,"The c.5465T>A variant in APC is a missense variant predicted to cause the substitution of Valine by Asparagine at amino acid position 1822 (p.Val1822Asp). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). The highest population minor allele frequency in gnomAD v2.1.1 is 0.9598 (23897/24898 alleles) in the African/African American population, which is higher than the ClinGen APC VCEP threshold (>0.1%) for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BA1 and BP1 (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.7862C>G,BA1;BS2;BP1,,0.667206287384033,BP1;BS2,,BA1,PM1;BP1;BS2,0.364747047424316,BS2;BP1,BA1,PM1,BA1;BP1,0.307969331741333,BP1;BA1,,BS2,"The c.7862C>G variant in APC is a missense variant predicted to cause the substitution of Serine by Cysteine at amino acid position 2621 (p.Ser2621Cys). This variant has been observed in more than 10 heterozygous individuals over the age of 50 with no features of FAP, worth more than 10 healthy individual points (BS2; Ambry internal data). APC is defined by the ClinGen APC VCEP as a gene for which primarily truncating variants are known to cause disease (BP1). The highest population minor allele frequency in the non-cancer cohort of gnomAD v2.1.1 is 0.5021% in the non-Finnish European population, which is higher than the ClinGen APC VCEP threshold of 0.1% for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as Benign for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: BA1, BS2, and BP1 (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_024675.3(PALB2):c.721A>G,BA1;BS2;BP1;BP2,,0.742187976837158,BP1;BS2,,BP2;BA1,BP1;BP4;BP6,0.376681089401245,BP1,BS2;BA1;BP2,BP6;BP4,BA1;BS2;BP1,0.300961971282959,BA1;BP1;BS2,,BP2,"The c.721A>G variant in PALB2 is a missense variant predicted to predicted to cause substitution of asparagine by aspartic acid at amino acid 241 (p.Asn241Asp). This variant has been observed in three homozygous individuals with no features of FANCN, a condition with full penetrance at an early age (Ambry Genetics). The highest population minor filtering allele frequency in gnomAD v2.1.1 is 0.005509 in the African population, which is higher than the HBOP VCEP threshold (>0.001) for BA1, and therefore meets this criterion. PALB2, in which the variant was identified, is defined by the HBOP VCEP as a gene for which primarily truncating variants are known to cause disease. In summary, this variant meets the criteria to be classified as benign for autosomal dominant hereditary breast and pancreatic cancer and autosomal recessive FANCN based on the ACMG/AMP criteria applied, as specified by the HBOP VCEP (BA1, BS2, BP1)",,, +NM_000038.6(APC):c.235A>G,PM2;BS2;BP1,,0.705420732498169,PM2;BS2,,BP1,PM1;PM2;BP1,0.358199596405029,BP1;PM2,BS2,PM1,BA1;BS2;BP1;BP2,0.311857223510742,BP1;BS2,BP2;BA1,PM2,"The c.235A>G variant in APC is a missense variant predicted to cause substitution of serine by glycine at amino acid 79 (p.Ser79Gly). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in 6 heterozygous individuals with no features of FAP, worth 3 healthy individual points (BS2_Supporting; Ambry Genetics Internal Data; Invitae Internal Data). In summary, this variant meets the criteria to be classified as Likely Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2_supporting, BP1. (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.420G>C,PM2;BS2;BP1;BP2,,0.696565866470337,BP1,,PM2;BS2,PM1;PM2;BP1,0.392112255096436,BP1;PM2,BS2;BP2,PM1,PM2;BS2;BP1,0.324557304382324,BP1;BS2;PM2,,BP2,"The c.420G>C variant in APC is a missense variant predicted to cause substitution of glutamic acid by aspartic acid at amino acid 140 (p.Glu140Asp). APCis defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in heterozygous state in 67 healthy unrelated adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics, Invitae, GeneDX internal data). This variant has also been observed in trans with a variant classified as (likely) pathogenic by the HCCP VCEP in an individual with FAP (BP2; Invitae Internal Data). Finally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as Likely Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2, BP1, BP2 (VCEP specifications version 1; date of approval 12/12/2022).",,, +NM_000038.6(APC):c.1487C>T,PM2;BS2;BP1,,0.791619539260864,BP1;PM2,,BS2,PM1;PM2;PP3;BP1,0.397652149200439,BP1;PM2,BS2,PP3;PM1,PM2;BS2;BP1;BP2,0.309634447097778,BP1;BS2;PM2,BP2,,"The c.1487C>T variant in APC is a missense variant predicted to cause substitution of threonine by isoleucine at amino acid 496 (p.Thr496Ile). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in a heterozygous state in 18 unrelated healthy adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics, Invitae, and GeneDX internal data). In summary, this variant meets the criteria to be classified as Likely Benign for FAP based on the ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2 and BP1 (VCEP specifications version 1.0, date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.4906G>T,PM2;BS2;BP1;BP2,PM1,8.05782437324524,PM2,PM1,BP1;BS2,PM1;PM2;PP3;BP1,0.36128044128418,BP1;PM2,BP2;BS2,PP3;PM1,PM2;BS2;BP1,0.346704483032226,BP1;BS2;PM2,,BP2,"The c.4906G>T variant in APC is a missense variant predicted to cause the substitution of aspartate by tyrosine at amino acid position 1636 (p.Asp1636Tyr). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant has been observed in trans with the variant c.3100G>T (p.Glu1034*) (Bonn internal data) which is classified as Pathogenic by the HCCP VCEP in an individual with FAP (BP2). This variant has been observed in heterozygous state in 11 unrelated healthy adult individuals worth ≥ 10 healthy individual points in total (BS2; Ambry Genetics internal data). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, although there are both pathogenic and benign types of evidence for this variant, the pathogenic/benign evidence is not considered inconsistent with the final Likely Benign classification for FAP. ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2, BP1, and BP2 (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_000038.6(APC):c.8438C>A,PM2;BS2;BP1,PM1;BP7,9.49743723869324,BP1;PM2,PM1;BP7,BS2,PM1;PM2;BP1,0.388001680374146,BP1;PM2,BS2,PM1,PM2;BS2;BP1;BP2,0.315003395080566,BP1;BS2;PM2,BP2,,"The c.8438C>A variant in APC is a missense variant predicted to cause the substitution of Threonine by Lysine at amino acid position 2813 (p.Thr2813Lys). This variant has been observed in ≥ 3 individuals with no features or family history of FAP, which is worth 3 healthy individual points (BS2_supporting; Invitae and Ambry internal data). APC is defined by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (HCCP VCEP) as a gene for which primarily truncating variants are known to cause disease (BP1). This variant is absent from gnomAD v2.1.1 (PM2_supporting). In summary, this variant meets the criteria to be classified as Likely Benign for FAP. Although there are both pathogenic and benign types of evidence for this variant, the pathogenic evidence is not considered inconsistent with the final classification. ACMG/AMP criteria applied, as specified by the HCCP VCEP: BS2_supporting, and BP1. (VCEP specifications version 1; date of approval: 12/12/2022).",,, +NM_000277.2(PAH):c.472C>T,PS3;PM2;PM3;PP3;PP4,PM1;PM2;PM5;PP3;BP4,7.82847857475281,PM2;PP3,PM1;PM5;BP4,PP4,PM1;PM2;PP5;BP1,0.374401569366455,PM2,PM3;PP3;PP4;PS3,PP5;BP1;PM1,PM2;BS2;BP1,0.340309619903564,PM2,BP1;BS2,PP3;PM3;PP4;PS3,"PAH-specific ACMG/AMP criteria applied: PM2: Extremely low frequency. ExAC MAF=0.00019.; PP3: Predicted deleterious in SIFT, Polyphen-2, MutationTaster. REVEL=0.939; PS3: 2% mutant enzyme activity in BioPKU; PP4_Moderate: Detected in at least 3 patients with PAH deficiency. BH4 deficiency ruled out in 1 patient. (PMID:1307609; PMID:10429004; PMID:9634518); PM3_Strong: Detected with 3 pathogenic/likely pathogenic variants (PMID:14681498; PMID:23430918). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PP3, PS3, PP4_Moderate, PM3_Strong).",,, +NM_000277.2(PAH):c.533A>G,PS3;PM2;PM3;PP3;PP4,PM1;PM2,7.92781496047974,PM2,PM1,PS3;PP3,PM1;PM2;PP3;PP5;BP1,0.379242897033691,PP3;PM2,PM3;PP4;PS3,PP5;BP1;PM1,PS3;PM2;PM3;PP3;PP4,0.284643173217773,PM3;PP3;PS3;PM2;PP4,,,"PAH-specific ACMG/AMP criteria applied: PM2: Absent from 1000G, ESP. ExAC MAF=0.00017; PP3: Deleterious effect predicted in SIFT, Polyphen2, MutationTaster. REVEL=0.841; PS3: 39% residual phenylalanine hydroxylase activity (PMID:17935162); PP4_Moderate: Detected in 6 PKU patients. BH4 deficiency excluded. Upgraded per ClinGen PAHEP. (PMID:18294361; PMID:9634518); PM3_Strong: In trans with 3 pathogenic variants (PMID:18294361). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PP3, PS3, PP4_Moderate, PM3_Strong).",,, +NM_000277.2(PAH):c.194T>C,PS3;PM3;PP3;PP4,PM1;PM2;PM5;PP3;BP4,7.47418713569641,PP3,PM1;PM5;BP4;PM2,PP4,PM1;PM2;PP3;PP5;BP1,0.358322143554687,PP3,PM3;PP4;PS3,PP5;BP1;PM1;PM2,PS3;PM2;PM3;PP3;PP4,0.296109437942505,PP3;PM3;PS3;PP4,PM2,,"PAH-specific ACMG/AMP criteria applied: PM3_VeryStrong: Detected with Y414C (P), R408W (P), P281L (P), IVS10nt-11 (P), R252W (P/LP), and R243Q(P). (PMID:12501224; PMID:1301201; PMID:10767174); PP3: Predicted dleterious in SIZFT, Polyphen2, MutationTaster. REVEL=0.985; PP4_Moderate: Detected in a patient with mild PKU. BH4 deficiency excluded. Upgraded per ClinGen PAH EP. (PMID:12501224); PS3: 25% mutant enzyme activity in COS cells as compared in wt (PMID:1301201). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM3_VeryStrong, PP3, PP4_Moderate, PS3).",,, +NM_004999.3(MYO6):c.1025C>T,PP3;BA1,PM2;BP7,4.69298410415649,BA1,PM2;BP7,,PM2;PP3;BP6;BS2,0.382071018218994,PP3,BA1,BS2;BP6;PM2,PM1;PM2;PM5;PP3;PP5,0.308812379837036,PP3,PM1;PM5;PP5;PM2,BA1,"The filtering allele frequency of the p.Ala342Val variant in the MYO6 gene is 0.21% for European (non-Finnish) chromosomes by gnomAD (304/129090 with 95% CI), and one homozygous European (Finnish) individual, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal dominant hearing loss variants (BA1). The REVEL computational prediction analysis tool produced a score of 0.905, however, this information is not predictive of pathogenicity on its own and is not considered in conflict with evidence that supports a benign interpretation. In summary, the HL EP classified this variant as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1.",,, +NM_000441.1(SLC26A4):c.1069G>A,PP3;BA1,PM1;PM2,14.513293504715,BA1,PM1;PM2,,PM1;PP3;BP1;BP6;BS2,1.34810471534729,PP3,BA1,BS2;BP1;BP6;PM1,PP3;BA1,0.313730001449585,PP3;BA1,,,"The filtering allele frequency of the p.Ala357Thr variant in the SLC26A4 gene is 0.47% for African chromosomes by gnomAD (136/24968 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive Pendred syndrome variants (BA1). The REVEL computational prediction analysis tool produces a score of 0.849, which is above the threshold necessary to apply PP3; however, this information is not predictive of pathogenicity on its own and is not considered in conflict with evidence that supports a benign interpretation. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1.",,, +NM_000527.5(LDLR):c.970G>A,PP1;PP3;BA1;BS2;BP2,,3.14010524749756,PP3;BA1;BS2,,PP1;BP2,PM1;PP2;PP3;BP1;BS1;BS2,0.426384925842285,PP3;BS2,BP2;PP1;BA1,PP2;BP1;PM1;BS1,PP3;BA1,0.330469131469726,PP3;BA1,,PP1;BP2;BS2,"The NM_000527.5(LDLR):c.970G>A (p.Gly324Ser) variant is classified as Benign for Familial Hypercholesterolemia by applying evidence codes (BA1, BS2, BP2, PP1 and PP3) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: BA1 - FAF = 0.01153 (1.153%) in African/African American exomes (gnomAD v2.1.1). BS2 - Identified in 4 heterozygous non-affected family members from different labs.BP2 - variant identified 1 index case with heterozygous FH phenotype who is double heterozygous with NM_000384.3(APOB):c.10580G>A p.Arg3527Gln (ClinVar ID 17890) - classified as Pathogenic by the general ACMG guidelines (Chora et al., 2018).PP1 - variant segregates with phenotype in 2 informative meiosis in 1 family from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge.PP3 - REVEL = 0.815.Variant has 1 stand alone, 1 Strong and 1 Supporting evidence codes towards Benign, enough to classify as Benign, and only 2 Supporting codes towards Pathogenic. The Benign criteria overwhelms the Pathogenic criteria, so we are confident in classifying this variant as Benign.",,, +NM_000441.1(SLC26A4):c.1363A>T,PP3;BA1,,0.686535835266113,PP3,,BA1,PM1;PP3;BP1;BP6;BS2,0.345483303070068,PP3,BA1,BS2;BP1;BP6;PM1,PP1;PP3;BA1;BS2;BP2,0.292094707489014,PP3;BA1,PP1;BP2;BS2,,"The filtering allele frequency of the p.Ile455Phe variant in the SLC26A4 gene is 3% (981/30778) of South Asian chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which is a high frequency that is consistent with benign classification based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1).",,, +NM_000545.8(HNF1A):c.1135C>G,PP3;BA1,,0.668957233428955,BA1,,,PM1;PM2;PP3,0.360151767730713,PP3,BA1,PM1;PM2,PP3;BA1,0.322887182235718,PP3;BA1,,,"The c.1135C>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of proline to alanine at codon 379 (p.(Pro379Ala)) of NM_000545.8. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.9639, which is greater than the MDEP VCEP threshold of 0.70 (PP3). While this variant has been identified in >20 unrelated individuals with diabetes in the literature (ClinVar ID 431970, PMID:18003757, PMID: 23348805, PMID: 29207974, PMID: 21761282, PMID: 23607861), it has a Popmax Filtering allele frequency in gnomAD 2.1.1 of 0.0005091, which is greater than the MDEP threshold for BA1 (greater than 0.0001) (BA1). Therefore, PS4 cannot be applied. While another variant at this codon, c.1136C>G (p.(Pro379Arg)), is classified as Pathogenic by the MDEP, the c.1135C>G meets the criteria to be classified as benign for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.1.1, approved 8/11/2023): BA1, PP3. It may, however, confer an increased risk of type 2 diabetes (OR = 11.8, p = 0.0007324 at type2diabetesgenetics.org).",,, +NM_000545.8(HNF1A):c.1136C>A,PM5;PP3;PP4;BA1,PM1;PM2;PM5;PP3;BP4,289.539047002792,PM5;PP3,PM1;BP4;PM2,BA1,PM1;PM2;PP3,0.405366659164429,PP3,PP4;PM5;BA1,PM1;PM2,PP3;BA1,0.37108302116394,PP3;BA1,,PM5;PP4,"The c.1136C>A variant in the HNF1 homeobox A gene, HNF1A causes an amino acid change of proline to histidine at codon 379 (p.(Pro379His)) of NM_000545.8. This variant has a Popmax Filtering allele frequency in gnomAD 2.1.1 of 0.0001567, which is greater than the MDEP threshold for BA1 (0.0001)(BA1). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.969, which is greater than the MDEP VCEP threshold of 0.70 (PP3). Functional studies demonstrated the p.Pro379His protein has transcriptional activity on insulin promoter 62% of WT in RINm5f cells and 78% of WT in HeLA cells (PMID 15883474). While one cell line is greater than the MDEP BS3 cutoff of 75%, one is between the ClinGen MDEP cutoffs for PS3 (<=40%) and BS3, and therefore neither PS3 nor BS3 is applied. This variant was identified in one family and segregated with diabetes with two informative meioses; however, this does not meet the thresholds for PP1 or PS4 set by the ClinGen MDEP (PMIDs: 27236918, 15883474). An individual in this family had a clinical history highly specific for HNF1A-monogenic diabetes (MODY probability calculator result >50%, negative genetic testing for HNF4A, and antibody negative) (PP4_Moderate; PMID 15883474). Another missense variant, c.1136C>G (p.Pro379Arg), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Pro379His (PM5_Supporting). In summary, c.1136C>A meets the criteria to be classified as benign for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.1.0, approved 8/11/2023): BA1, PM5_Supporting, PP4_Moderate, PP3.",,, +NM_001110792.2(MECP2):c.968C>T,PP3;BS1;BS2;BP5,PM1;PM2,7.84452056884766,BS2,PM1;PM2,PP3;BS1,PM1;PM2;PP3;BP1,0.363806486129761,PP3,BS2;BP5;BS1,PM1;BP1;PM2,PM5;PP3;PP4;BA1,0.296879529953003,PP3,PM5;PP4;BA1,BS1;BP5;BS2,"The allele frequency of the p.Thr311Met variant in MECP2 (NM_004992.3) is 0.022% and 0.01% in ""Other"" and South Asian sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Thr311Met variant is observed in at least 2 unaffected individuals (GeneDx internal database) (BS2) and found in 2 patients with an alternate molecular basis of disease (Baylor Genetics internal database, Invitae internal database) (BP5). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own (PP3). As this variant meets 2 strong and 1 supporting benign criteria it can be classified as benign even though in silico predictions meet PP3. In summary, the p.Thr311Met variant in MECP2 is classified as benign for Rett syndrome based on the ACMG/AMP criteria (BS1, BS2, BP5).",,, +NM_004985.4(KRAS):c.15A>T,PS4;PM2;PM6;PP2;PP3,PS1;PP3;BP4,15.3030745983124,PM2;PP3,PS1;BP4,PP2;PM6,PM1;PM2;PP3;PP5,0.365798234939575,PP3;PM2,PM6;PS4;PP2,PM1;PP5,PP3;BS1;BS2;BP5,0.289863109588623,PP3,BS1;BP5;BS2,PP2;PM6;PS4;PM2,"The c.15A>T (p.Lys5Asn) variant in KRAS has been reported in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID: 17056636, GeneDx internal data). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The p.Lys5Asn variant has been identified in at least 4 independent occurrences in patients with a RASopathy (PS4_Moderate; PMID: 17056636, GeneDx, EGL Genetics internal data, ClinVar SCV000202928.7). Computational prediction tools and conservation analysis suggest that the p.Lys5Asn variant may impact protein function (PP3). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM6_Strong, PM2, PP2, PP3.",,, +NM_004333.4(BRAF):c.1785T>G,PS4;PM1;PM2;PM6;PP2;PP3,PS1;PM1;PP3;BP4,12.6560122966766,PP2;PM1;PP3,PS1;BP4,PM2;PS4,PM1;PM2;PP5,0.367579221725464,PM1;PM2,PM6;PS4;PP3;PP2,PP5,PS4;PM2;PM6;PP2;PP3,0.336376667022705,PM6;PP3;PP2;PM2;PS4,,PM1,"The c.1785T>G (p.Phe595Leu) variant in BRAF has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID 19206169, 18042262; GTR ID's: 26957, 21766; ClinVar SCV000203922.4, SCV000207755.12). The variant has also been identified in at least 2 independent occurences in patients with clinical features of a RASopathy (PS4_Supporting; APHP-Robert Debré internal data; GTR ID 28338). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581, 16439621). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Phe595Leu variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PM6_Strong, PM2, PM1, PP2, PP3, PS4_Supporting.",,, +NM_004985.4(KRAS):c.101C>T,PS2;PM2;PM5;PP2;PP3,,4.86893200874329,PP2;PM2;PM5,,PS2;PP3,PM1;PM2;PP3;PP5,0.38914942741394,PP3;PM2,PP2;PS2;PM5,PM1;PP5,PS4;PM1;PM2;PM6;PP2;PP3,0.302638530731201,PP3;PP2;PM2,PM1;PM6;PS4,PS2;PM5,"The c.101C>T (p.Pro34Leu) variant in KRAS has been reported as a confirmed de novo occurrence in a patient with clinical features of a RASopathy (PS2; PMID 17056636, 20949621). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). A different pathogenic missense variant has been previously identified at this codon of KRAS which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 12590). Computational prediction tools and conservation analysis suggest that the p.Pro34Leu variant may impact the protein (PP3; PMID: 24803665). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PS2, PM2, PM5, PP3, PP2.",,, +NM_004985.4(KRAS):c.173C>T,PS3;PM1;PM2;PM6;PP2;PP3,,0.658904314041138,PP2;PM2;PP3,,PM1;PM6,PM1;PM2;PP3;PP5,0.357168197631836,PM1;PP3;PM2,PS3;PP2;PM6,PP5,PS2;PM2;PM5;PP2;PP3,0.306113719940185,PP3;PP2;PM2,PS2;PM5,PM1;PM6;PS3,"The c.173C>T (p.Thr58Ile) variant in KRAS has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6_Strong; PMID 23321623, 20112233, 16921267, 16474405, 22488832, 18247425, 20949621). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). In vitro functional studies provide some evidence that the p.Thr58Ile variant may impact protein function (PS3; PMID: 23321623, 20949621, 16921267). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of KRAS (PM1; PMID 29493581). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Thr58Ile variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6_Strong, PS3, PM2, PM1, PP2, PP3.",,, +NM_176795.4(HRAS):c.173C>T,PS1;PS4;PM1;PM2;PM6;PP2;PP3,,0.674533367156982,PP2;PP3;PS1,,PM1;PS4;PM2,PM1;PM2;PP3;PP5,0.37951135635376,PM1;PP3;PM2,PM6;PS4;PS1;PP2,PP5,PS3;PM1;PM2;PM6;PP2;PP3,0.538906812667847,PM6;PP3;PP2;PM2;PM1,PS3,PS4;PS1,"The c.173C>T (p.Thr58Ile) variant in HRAS has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; PMID 20112233, 16474405). Also, at least 2 independent occurrences of this variant have been detected in patients with a RASopathy (PS4_Supporting; PMID: 22488832, 18247425, 23321623, 20949621, 16921267). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The p.Thr58Ile variant in HRAS is analogous to the same previously established amino acid change in the KRAS gene and the ClinGen RASopathy Expert Panel has defined that the pathogenicities of analogous variants in the HRAS and KRAS genes are correlated based on the assumption that a known functional residue in one gene is equivalent to other functions within that subgroup (PS1; 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of HRAS (PM1; PMID 29493581). The variant is in HRAS, which has been defined by the ClinGen RASopathy Expert Panel as a gene with low rate of benign missense with missense variants commonly being pathogenic (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Thr58Ile variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6, PS4_Supporting, PM2, PS1, PM1, PP2, PP3.",,, +NM_005343.3(HRAS):c.350A>G,PS3;PM1;PM2;PM6;PP3,,0.758193969726563,PM1;PP3,,PM6;PM2,PM1;PM2;PP3;PP5,0.36811375617981,PM1;PP3;PM2,PS3;PM6,PP5,PM1;PM2;PP3;PP5,0.311939001083374,PP3;PM1;PM2,PP5,PM6;PS3,"The c.350A>G (p.Lys117Arg) variant in HRAS has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID 16443854, 16155195). In vitro functional studies provide some evidence that the p.Lys117Arg variant may impact protein function (PS3; PMID 17979197, 21850009). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of HRAS (PM1; PMID 29493581). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Computational prediction tools and conservation analysis suggest that the p.Lys117Arg variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PM6_Strong, PS3, PM1, PM2, PP3.",,, +NM_005633.3(SOS1):c.1642A>C,PS2;PS3;PM1;PM2;PP2;PP3,,0.665717363357544,PP2;PM1;PM2,,PS2;PP3,PM1;PM2;PP3;PP5,0.362068653106689,PM1;PP3;PM2,PS3;PS2;PP2,PP5,PM1;PM2;PP3;PP5,0.320886850357056,PP3;PM1;PM2,PP5,PP2;PS2;PS3,"The c.1642A>C (p.Ser548Arg) variant in SOS1 has been reported as a confirmed de novo occurrence in a patient with clinical features of a RASopathy (PS2_VeryStrong; PMID 17143282). In vitro functional studies provide some evidence that the p.Ser548Arg variant may impact protein function (PS3; PMID 23487764). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of SOS1 (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Ser548Arg variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID: 29493581): PP2, PP3, PM1, PM2, PS3 PS2_VeryStrong.",,, +NM_005633.3(SOS1):c.806T>C,PS2;PM1;PM2;PP2;PP3,,0.658915042877197,PP2;PM1;PM2,,PS2;PP3,PM1;PM2;PP3;PP5,0.45712423324585,PM1;PP3;PM2,PP2;PS2,PP5,PS2;PS3;PM1;PM2;PP2;PP3,0.381702899932861,PP3;PP2;PM2;PS2;PM1,PS3,,"The c.806T>C (p.Met269Thr) variant in SOS1 has been reported in the literature in at least 2 unconfirmed and 1 confirmed de novo occurrences in patients with clinical features of a RASopathy (PS2_VeryStrong; PMID 17586837; 19953625, 20683980). It has also been reported as a confirmed de novo occurrence in a patient with clinical features of a RASoapthy (PMID: 20683980). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is in SOS1, which has been defined by the ClinGen RASopathy Expert Panel as a gene with low rate of benign missense with missense variants commonly being pathogenic (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Met269Thr variant may impact the protein (PP3). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of SOS1 (PM1; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID: 29493581): PP2, PP3, PM1, PM2, PS2_VeryStrong.",,, +NM_002880.3(RAF1):c.1472C>T,PS3;PM1;PM2;PP2;PP3,PM1;PM5;PP3;BP4,8.11765480041504,PP2;PM1;PP3;PM2,PM5;BP4,PS3,PM1;PM2;PP3;PP5,0.383171319961548,PM1;PM2;PP3,PP2;PS3,PP5,PS2;PM1;PM2;PP2;PP3,0.313710212707519,PP3;PM1;PP2;PM2,PS2,PS3,"The c.1472C>T (p.Thr491Ile) variant in RAF1 has been reported in the literature in at least one individual with clinical features of a RASopathy (PS4 not met; PMID 17603483). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Thr491Ile variant may impact the protein (PP3). In vitro functional studies provide some evidence that the p.Thr491Ile variant may impact protein function (PS3; 20679480). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of RAF1 (PM1; PMID 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PP2, PP3, PM1, PM2, PS3.",,, +NM_002755.3(MAP2K1):c.389A>G,PS2;PS3;PM1;PM2;PP2;PP3,PM1;PP3;BP4,7.968829870224,PP2;PM1;PP3,BP4,PM2;PS2,PM1;PM2;PP2;PP3;PP5,0.403749942779541,PM1;PM2;PP2;PP3,PS2;PS3,PP5,PS3;PM1;PM2;PP2;PP3,0.296164512634277,PP3;PS3;PP2;PM2;PM1,,PS2,"The c.389A>G (p.Tyr130Cys) variant in MAP2K1 has been reported as a confirmed de novo occurrence in at least 2 patients with clinical features of a RASopathy (PS2_VeryStong; PMID 16439621, 17551924, 18042262). In vitro functional studies provide some evidence that the p.Tyr130Cys variant may impact protein function (PS3; PMID 18413255, 23093928, 17981815). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the MAP2K1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of MAP2K1 (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Tyr130Cys variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PP3, PS3, PM2, PP2, PM1.",,, +NM_002755.3(MAP2K1):c.275T>G,PS2;PS4;PM2;PP2;PP3,PM1,7.97276663780212,PP2,PM1,PM2;PP3,PM1;PM2;PP2;PP3;PP5,0.395981073379517,PM2;PP2;PP3,PS2;PS4,PM1;PP5,PS2;PS3;PM1;PM2;PP2;PP3,0.30141806602478,PP3;PP2;PS2;PM2,PM1;PS3,PS4,"The c.275T>G (p.Leu92Arg) variant in MAP2K1 has been reported in at least 3 de novo occurrences, including 1 case with parental confirmation, in patients diagnosed with a RASopathy (PS2_VeryStrong, PS4_Moderate; GeneDx, APHP-Robert Debre hospital, Laboratory for Molecular Medicine internal data; ClinVar SCV000207940.11, SCV000965969.1, SCV000061251.5). This variant was absent from large population studies (PM2; gnomad.broadinstitute.org). The variant is located in the MAP2K1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Leu92Arg variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PS4_Moderate, PM2, PP2, PP3.",,, +NM_000277.2(PAH):c.529G>A,PM2;PM3;PM5;PP3;PP4,PM1;PM2;PM5,8.22266864776611,PM5;PM2,PM1,PP3,PM1;PM2;PP3;PP5;BP1,0.469707727432251,PM2;PP3,PM3;PM5;PP4,PM1;BP1;PP5,PS2;PS4;PM2;PP2;PP3,0.281403064727783,PP3;PM2,PP2;PS2;PS4,PM3;PP4;PM5,"The c.529G>A (p.Val177Met) variant in PAH was detected in a patient with Mild hyperphenylalaninemia (BH4 deficiency ruled out). PMID: 12501224 It has been detected with known pathogenic variants R408W (PMID: 12501224), and IVS12+1G>A (PMID: 23764561). It is absent from 1000G, ESP, and gnomAD; and at extremely low frequency in ExAC (MAF=0.00003). A deleterious effect is predicted in SIFT, Polyphen-2, MutationTaster, and REVEL=0.89. A different pathogenic missense change has been seen at this amino acid (V177L). In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM3_strong, PM2, PM5, PP4_Moderate, PP3.",,, +NM_000277.2(PAH):c.848T>A,PM2;PM3;PM5;PP3;PP4,PM1,8.48596286773682,PM5;PP3,PM1,PM2;PM3,PM1;PM2;PP3;PP5;BP1,0.480615854263306,PM2;PP3,PM3;PM5;PP4,PM1;BP1;PP5,PM2;PM3;PM5;PP3;PP4,0.317513227462768,PM3;PM5;PP3;PM2;PP4,,,"The c.848T>A (p.Ile283Asn) variant in PAH is absent from population databases and predicted damaging with in silico predictors. It is a novel missense change in a residue where a different pathogenic variant has been identified (c.847A>T (p.Ile283Phe). It has been identified in multiple affected individuals in trans with known pathogenic variants (PMID: 9521426, 26413448), and was identified in a patient in which a defect in BH4 metabolism had been excluded. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM3_strong, PM2, PM5, PP4_Moderate, PP3.",,, +NM_000277.2(PAH):c.799C>G,PS3;PM2;PM3;PP3;PP4,PM1;PP3;BP4,14.820294380188,PP3,PM1;BP4,PM2;PP4,PM1;PM2;PP3;PP5;BP1,0.417472362518311,PM2;PP3,PM3;PS3;PP4,PM1;BP1;PP5,PM2;PM3;PM5;PP3;PP4,0.302389144897461,PP3;PM3;PP4;PM2,PM5,PS3,"The c.799C>G (p.Gln267Glu) variant in PAH was reported in 2 Chinese PKU patients. BH4 deficiencies not completely ruled out. (PMID: 26600521) This variant was detected with known pathogenic variants p.R111X (PMID: 16256386), and D101N (not in ClinVar, PMID: 26600521). It is absent from ExAC, gnomAD, 1000G, and ESP. This variant is predicted deleterious in SIFT, Polyphen2, MutationTaster, and REVEL=0.935. This variant was expressed in e. coli using a rat Q267E mutant. It has 11% activity of wt. based on duplicate determinations of a single clone. (PMID: 7914195). In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM2, PM3, PS3, PP3, PP4.",,, +NM_004086.2(COCH):c.151C>T,PS4;PM2;PP1;PP3,,3.88356995582581,PM2,,PS4;PP3,PM1;PM2;PP2;PP3;PP5,0.443260192871094,PM2;PP3,PP1;PS4,PM1;PP2;PP5,PS3;PM2;PM3;PP3;PP4,0.314664840698242,PP3;PM2,PM3;PP4;PS3,PP1;PS4,"The c.151C>T (p.Pro51Ser) variant in COCH has been reported to segregate with late onset progressive hearing loss and vestibular dysfunction in > 25 family members (PP1_S; PMID: 9931344, 11332404). The variant meets PM2 and has been observed in at least 15 affected probands (PS4, PMID: 28733840, 16151338, 11332404). The allele frequency of the p.Pro51Ser variant is 0.001% (1/111716) of European chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org), which is a low enough frequency to award PM2 based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal dominant hearing loss (PM2). Computational prediction tools and conservation analysis suggest that the p.Pro51Ser variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hearing loss based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PP1_S, PS4, PM2, PP3.",,, +NM_000277.2(PAH):c.1278T>C,BA1;BP4,,0.85227108001709,BP4,,BA1,BP4;BP6;BP7;BS1,0.39901065826416,BP4,BA1,BP6;BP7;BS1,PS4;PM2;PP1;PP3,0.304616212844849,,PP3;PP1;PS4;PM2,BP4;BA1,"PAH-specific ACMG/AMP criteria applied: BA1: MAF=0.16641; BP4: no impact on gene in SIFT, Polyphen2, MutationTaster. In summary this variant meets criteria to be classified as benign for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (BA1, BP4).",,, +NM_000277.2(PAH):c.707-7A>T,BA1;BP4,PVS1,0.943348407745361,BP4,PVS1,BA1,,0,,,,BA1;BP4,0.318448066711426,BP4;BA1,,,"PAH-specific ACMG/AMP criteria applied: BA1: Highest MAF=0.10514 in 1000G. 35 homozygotes in ExAC; BP4: HSF: No significant splicing motif alteration detected. This mutation has probably no impact on splicing. CADD=1.163344. In summary this variant meets criteria to be classified as benign for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (BA1, BP4).",,, +NM_000277.2(PAH):c.735G>A,BA1;BS2;BP4,,0.67733359336853,BA1;BP4,,,BA1;BP4;BP7;BS1,0.365957736968994,BA1;BP4,BS2,BS1;BP7,BA1;BP4,0.315269947052002,BP4;BA1,,BS2,"The c.735G>A (p.Val245=) variant in PAH has a MAF of 0.29058 in ExAC (BA1; http://exac.broadinstitute.org) with 6,524 homozygotes (BS2). This is a synonymous variant, predicted tolerated and benign in SIFT, Polyphen. MutationTaster predicted polymorphism with no abrogation of splice sites (BP4). In summary, this variant meets criteria to be classified as benign.",,, +NM_005633.3(SOS1):c.1230G>A,BA1;BP4;BP5;BP7,PM2;BP7,2.09849143028259,BP7;BP4,PM2,BA1,BP4;BP6;BP7;BS1;BS2,0.392003297805786,BP4;BP7,BP5;BA1,BS2;BS1;BP6,BA1;BS2;BP4,0.311575174331665,BP4;BA1,BS2,BP5;BP7,"The c.1230G>A (p.Gln410=) variant in SOS1 has been identified in a patient with an alternate molecular basis for disease (BP5; Partners LMM internal data GTR Lab ID: 21766 ClinVar SCV000062189.5). This variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Computational prediction tools and conservation analysis suggest that the p.Gln410= variant does not impact the protein (BP4). The filtering allele frequency of the c.1230G>A (p.Gln410=) variant in the SOS1 gene is 4.69% for Latino chromosomes by the Exome Aggregation Consortium (580/11526 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP5, BP7, BP4.",,, +NM_007373.3(SHOC2):c.1302C>T,BA1;BP4;BP5;BP7,PM2,2.26057815551758,BP4,PM2,BP7;BA1,BP4;BP6;BP7,0.50866961479187,BP4;BP7,BP5;BA1,BP6,BA1;BP4;BP5;BP7,0.321614265441894,BP4;BP5;BP7;BA1,,,"The c.1302C>T (p.Asn434=) variant in the SHOC2 gene has been identified in a patient with an alternate molecular basis for disease (BP5; ClinVar SCV000171633.12). The silent p.Asn434= variant is not predicted by MaxEntScan to impact splicing (BP7, BP4).The filtering allele frequency of the c.1302C>T (p.Asn434=) variant is 0.74% for African chromosomes by the Exome Aggregation Consortium (87/9772 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP5, BP4, BP7.",,, +NM_002834.4(PTPN11):c.1658C>T,BA1;BP4,PM2;BP7,8.43284821510315,BA1,PM2;BP7,,PM1;PM2;BP6;BS2,0.362895965576172,,BP4;BA1,PM2;BS2;PM1;BP6,BA1;BP4;BP5;BP7,0.296144723892212,BP4;BA1,BP5;BP7,,"The filtering allele frequency of the c.1658C>T (p.Thr553Met) variant in the PTPN11 gene is 0.048% for European (Non-Finnish) chromosomes by the Exome Aggregation Consortium (49/66556 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). Computational prediction tools and conservation analysis suggest that the p.Thr553Met variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP4.",,, +NM_004333.4(BRAF):c.1227A>G,BA1;BP4;BP5;BP7,PM2,1.99128532409668,BP7;BP4,PM2,BA1;BP5,BP4;BP6;BP7;BS1;BS2,0.41414737701416,BP4;BP7,BP5;BA1,BS2;BS1;BP6,BA1;BP4,0.30139946937561,BP4;BA1,,BP5;BP7,"The filtering allele frequency of the c.1227A>G (p.Ser409=) variant in the BRAF gene is 0.313% for European (Non-Finnish) chromosomes by the Exome Aggregation Consortium (233/66620 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). Additionally, this variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). The p.Ser409= variant has been identified in a patient with an alternate molecular basis for disease (BP5; GeneDx, Partners LMM, EGL Genetics internal data; GTR ID's: 21766, 26957, 500060; SCV000057203.8; SCV000061570.5; SCV000112807.7). Computational prediction tools and conservation analysis suggest that the p.Ser409= variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied: BA1, BP7, BP5, BP4.",,, +NM_001754.4(RUNX1):c.614-34C>T,BA1;BP2;BP4,BP7,2.41879773139954,BP4,BP7,BA1,,0,,,,BA1;BP2;BP4,0.300057888031006,BP2;BP4;BA1,,,"The NM_001754.4:c.614-34C>T variant has a MAF of 1 (100%) in gnomAD cohort that is ≥ 0.0015 (0.15%) (BA1). This variant is detected in homozygous state in gnomAD population database (BP2). This intronic variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created (BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4.",,, +NM_000441.2(SLC26A4):c.416-7T>C,BA1;BP4;BP7,PM1;PM2;BP7,1.94276523590088,BP7;BA1,PM1;PM2,,,0,,,,BA1;BP4;BP7,0.325613260269165,BP4;BP7;BA1,,,"The filtering allele frequency of the c.416-7T>C variant in SLC29A4 is 0.59% (169/24960) in African chromosomes in gnomAD (BA1). Additionally, computational prediction tools and conservation analysis suggest that the c.416-7T>C variant may not impact the protein (BP4, BP7). In summary, this variant meets criteria to be classified as benign for autosomal recessive Pendred syndrome. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP7, BP4.",,, +NM_005633.3(SOS1):c.*4C>T,BA1;BP4;BP7,PM2;BP7,5.61773633956909,BP7;BA1,PM2,,,0,,,,BA1;BP4;BP7,0.299153566360474,BP4;BP7;BA1,,,"The c.*4C>T variant in SOS1 is classified as benign because it has been identified in 0.05383% (95% CI of 27/35402) of Latino alleles in gnomAD (BA1; https://gnomad.broadinstitute.org). It does not alter an amino acid residue, is not located within the splice consensus site, and computational splice prediction tools do not predict an impact on splicing (BP4, BP7). ACMG/AMP Criteria applied: BA1, BP4, BP7.",,, +NM_004985.5(KRAS):c.-160A>G,BA1;BP4;BP7,BP7,1.81799578666687,BP7;BP4,,BA1,,0,,,,BA1;BP4;BP7,0.30588436126709,BP4;BP7;BA1,,,"The c.-160A>G variant in KRAS is classified as benign because it has been identified in 0.22088% (95% CI of 27/8628) of African alleles in gnomAD (BA1; https://gnomad.broadinstitute.org). This variant is not located within the splice consensus sequence and computational splice site prediction tools do not predict an impact on splicing (BP4, BP7). ACMG/AMP Criteria applied: BA1, BP4, BP7.",,, +NM_001754.4(RUNX1):c.1086G>C,BA1;BP4;BP7,PM2;BP7,1.88257908821106,BP7;BP4,PM2,BA1,BP4;BP6;BP7;BS2,0.373845815658569,BP7;BP4,BA1,BS2;BP6,BA1;BP4;BP7,0.31194543838501,BP4;BP7;BA1,,,"This synonymous variant has a MAF of 0.002828 (0.2828%, 61/21570, 43140 alleles) in the African (gnomAD) cohort is ≥ 0.0015 (0.15%) (BA1). It is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created; in addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -0.12 < 0.1 [-14.1;6.4]) (BP4+BP7). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP4, and BP7.",,, +NM_001754.4(RUNX1):c.423G>A,BS1;BP4;BP7,PM1;PM2,1.53935885429382,BP7;BP4,PM1;PM2,BS1,PM2;BP4;BP6;BP7,0.361729860305786,BP7;BP4,BS1,PM2;BP6,BS1;BP4;BP7,0.313875436782837,BS1;BP4;BP7,,,"The MAF of the NM_001754.4(RUNX1):c.423G>A (p.Ser141=) variant is 0.0001633 (0.016%, 5/30614 alleles, 251394 alleles) in the South Asian cohort (gnomAD), which is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created (BP4). In addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score: -1.49 < 0.1 [-14.1;6.4]) (BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BS1, BP4, and BP7.",,, +NM_000546.5(TP53):c.704A>G,BS1;BS2;BS3;BS4;BP2;BP4,PM1;PM2,1038.8517036438,BS1;BS2,PM1;PM2,BS4;BP4,PM1;PM2;PP3;BP6,0.399460077285767,,BP2;BP4;BS3;BS2;BS4;BS1,PM2;BP6;PM1;PP3,BS1;BS2;BS3;BS4;BP2;BP4,0.297839879989624,BP2;BS3;BS2;BS4;BS1;BP4,,,"This variant has a minor allele frequency of 0.0003175 (0.03%, 41/129,118 alleles) in the European (non-Finnish) subpopulation of the gnomAD cohort (BS1). The variant has a BayesDel score < 0.16 and Align GVGD (Zebrafish) is Class C0 or Class C15 (BP4). Additionally, transactivation assays show retained function according to Kato, et al. and there is no evidence of a dominant negative effect or loss of function according to Giacomelli, et al. (BS3; PMID: 12826609, 30224644). This variant also segregates to the opposite side of a family who meets Li-Fraumeni syndrome criteria. (BS4; PMID: 17318340). The proband in this same family has a pathogenic variant (TP53 c.560-1G>A) in trans with this variant. (BP2; PMID: 17318340). Finally, this variant has been observed in at least 4 60+ year old females without a cancer diagnosis (BS2_Supporting; FLOSSIES database - https://whi.color.com).In summary, TP53 c.704A>G; p.Asn235Ser meets criteria to be classified as benign for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: BS1, BP4, BS3, BS4, BP2, BS2_Supporting.",,, +NM_000546.5(TP53):c.935C>G,BS1;BS3;BP4,PM1;PM2,1030.96031284332,BP4;BS1,PM1;PM2,BS3,PM1;PM2;PP3;BP6;BS2,0.386345863342285,,BS3;BP4;BS1,PM2;BP6;PP3;BS2;PM1,BS1;BS3;BP4,0.315615653991699,BS1;BP4;BS3,,,"This variant has an allele frequency of 0.0003605 (0.03%, 9/24,966 alleles) in the African subpopulation of the gnomAD cohort (BS1). This variant also has a BayesDel score < 0.16 and Align GVGD (Zebrafish) is Class C0 or Class C15 (BP4). Additionally, transactivation assays show retained function according to Kato, et al. and there is no evidence of a dominant negative effect or loss of function according to Giacomelli, et al. (BS3; PMID: 12826609, 30224644). In summary, TP53 c.935C>G; p.Thr312Ser meets criteria to be classified as benign for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: BS1, BP4, BS3.",,, +NM_000546.5(TP53):c.869G>A,BS1;BS2;BS3;BP4,PM1;PM2,1062.64483118057,BP4;BS1,PM1;PM2,BS3;BS2,PM1;PM2;BP6;BS2,0.402278184890747,BS2,BS3;BP4;BS1,PM2;BP6;PM1,BS1;BS2;BS3;BP4,0.297675371170044,BS1;BP4;BS3;BS2,,,"This variant has a minor allele frequency of 0.0003583 (0.03%, 9/25,120 alleles) in the European Finnish subpopulation of the gnomAD cohort (BS1). Transactivation assays show super transactivation function according to Kato, et al. and there is no evidence of a dominant negative effect or loss of function according to Giacomelli, et al. (BS3; PMID: 12826609, 30224644). Additionally, this variant has a BayesDel score < 0.16 and Align GVGD (Zebrafish) is Class C0 or Class C15 (BP4). Finally, this variant has been observed in at least 7 60+ year old females without a cancer diagnosis (BS2_Supporting; FLOSSIES database - https://whi.color.com). In summary, TP53 c.869G>A; p.Arg290His meets criteria to be classified as benign for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: BS1, BS3, BP4, BS2_Supporting.",,, +NM_000441.2(SLC26A4):c.1708-18T>A,BA1;BP4;BP7,PM1;BS1;BS2,2.56100249290466,BP7;BA1,PM1;BS1;BS2,,,0,,,,BA1;BP4;BP7,0.300298929214477,BP4;BP7;BA1,,,"The filtering allele frequency (the lower threshold of the 95% CI of 1456/25104) of the c.1708-18T>A variant in the SLC26A4 gene is 5.55% for European (Finnish) chromosomes by gnomAD v2.1.1, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). This silent variant in SLC26A4 is not predicted by the computational prediction analysis using MaxEntScan to impact splicing (BP7, BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP7, BP4.",,, +NM_005249.4(FOXG1):c.209_232del24,BA1;BS2;BP3;BP5,PM1;PM2;BP3;BP7,1.16009497642517,BP3,BA1;BP5;BS2,PM1;PM2;BP7,,0,,,,PM2,0.251777172088623,,PM2,BA1;BP3;BP5;BS2,"The allele frequency of the p.Q70_P77del variant in FOXG1 is 0.03% in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The p.Q70_P77del variant is observed in at least 2 unaffected individuals (internal database) (BS2). The p.Q70_P77del variant is an in-frame deletion present in a repetitive region of FOXG1 (BP3). The p.Q70_P77del variant is found in at least 3 patients with an alternate molecular basis of disease (internal database) (BP5_strong). In summary, the p.Q70_P77del variant in FOXG1 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP3, BP5_strong).","{'pvs1': {'name': 'PVS1', 'prediction': , 'summary': '', 'description': 'PVS1 prediction failed.'}, 'ps1': {'name': 'PS1', 'prediction': , 'summary': 'Error occurred during PS1/PM5 prediction. Error: No valid primary variant information for PS1/PM5 prediction.', 'description': ''}, 'ps2': {'name': 'PS2', 'prediction': , 'summary': '', 'description': ''}, 'ps3': {'name': 'PS3', 'prediction': , 'summary': '', 'description': ''}, 'ps4': {'name': 'PS4', 'prediction': , 'summary': '', 'description': ''}, 'pm1': {'name': 'PM1', 'prediction': , 'summary': 'Counting pathogenic variants in the range of 50bp.The range is 29236654 - 29236704. => \nFound 4 Pathogenic variants. => \nFound 4 or more pathogenic variants. PM1 is met.', 'description': ''}, 'pm2': {'name': 'PM2', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAllele frequency: 0.0001351529936073348.\nAllele frequency <= 1%: PM2 is met.Check zygosity.\n', 'description': ''}, 'pm3': {'name': 'PM3', 'prediction': , 'summary': '', 'description': ''}, 'pm4': {'name': 'PM4', 'prediction': , 'summary': 'Check consequences of the variant for PM4.\nVariant consequence is in-frame deletion/insertion.\nCheck if the variant is in a repeat region.\nVariant is not in a repeat region.\nVariant is not in a repeat region or a conserved domain. PM4 is met.', 'description': ''}, 'pm5': {'name': 'PM5', 'prediction': , 'summary': 'Error occurred during PS1/PM5 prediction. Error: No valid primary variant information for PS1/PM5 prediction.', 'description': ''}, 'pm6': {'name': 'PM6', 'prediction': , 'summary': '', 'description': ''}, 'pp1': {'name': 'PP1', 'prediction': , 'summary': '', 'description': ''}, 'pp2': {'name': 'PP2', 'prediction': , 'summary': 'Fetching transcript data. => \nError occurred during PP2 and BP1 prediction. Error: Transcript data is not fully set. Cannot initialize the PVS1 class.', 'description': ''}, 'pp3': {'name': 'PP3', 'prediction': , 'summary': 'Checking Scores. => \nAn error occurred during prediction. Error: Missing dbNSFP data.', 'description': ''}, 'pp4': {'name': 'PP4', 'prediction': , 'summary': '', 'description': ''}, 'pp5': {'name': 'PP5', 'prediction': , 'summary': '', 'description': ''}, 'ba1': {'name': 'BA1', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAllele frequency: 0.0001351529936073348.\nAllele frequency <= 1%: PM2 is met.Check zygosity.\n', 'description': ''}, 'bs1': {'name': 'BS1', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAllele frequency: 0.0001351529936073348.\nAllele frequency <= 1%: PM2 is met.Check zygosity.\n', 'description': ''}, 'bs2': {'name': 'BS2', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAllele frequency: 0.0001351529936073348.\nAllele frequency <= 1%: PM2 is met.Check zygosity.\n', 'description': ''}, 'bs3': {'name': 'BS3', 'prediction': , 'summary': '', 'description': ''}, 'bs4': {'name': 'BS4', 'prediction': , 'summary': '', 'description': ''}, 'bp1': {'name': 'BP1', 'prediction': , 'summary': '', 'description': ''}, 'bp2': {'name': 'BP2', 'prediction': , 'summary': '', 'description': ''}, 'bp3': {'name': 'BP3', 'prediction': , 'summary': 'Check consequences of the variant for PM4.\nVariant consequence is in-frame deletion/insertion.\nCheck if the variant is in a repeat region.\nVariant is not in a repeat region.\nVariant is not in a repeat region or a conserved domain. PM4 is met.', 'description': ''}, 'bp4': {'name': 'BP4', 'prediction': , 'summary': 'Checking Scores. => \nAn error occurred during prediction. Error: Missing dbNSFP data.', 'description': ''}, 'bp5': {'name': 'BP5', 'prediction': , 'summary': '', 'description': ''}, 'bp6': {'name': 'BP6', 'prediction': , 'summary': '', 'description': ''}, 'bp7': {'name': 'BP7', 'prediction': , 'summary': 'Checking for pathogenic variants in the range of 2bp. => \nNo pathogenic variants found in the range of 2bp. => \nChecking for proximity to splice site. => \nVariant is not within 2bp of a splice site. => \nPredicting splice site alterations using SpliceAI. => \nVariant is not a splice site alteration. BP7 is met.', 'description': ''}}",,"{""variants"": [{""chr"": ""14"", ""pos"": 29236679, ""ref"": ""TCAAGAATATTAGTAGAAGCAGAAA"", ""alt"": ""T"", ""transcript"": ""ENST00000652140.1"", ""consequences_refseq"": [{""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 7, ""gene_symbol"": ""LOC102724934"", ""hgvs_c"": ""n.766-25289_766-25266delTTTCTGCTTCTACTAATATTCTTG"", ""transcript"": ""XR_001750707.2"", ""cds_start"": -4, ""cdna_length"": 1057}, {""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 4, ""gene_symbol"": ""LOC102724934"", ""hgvs_c"": ""n.1054-25289_1054-25266delTTTCTGCTTCTACTAATATTCTTG"", ""transcript"": ""XR_007064104.1"", ""cds_start"": -4, ""cdna_length"": 1482}], ""consequences_ensembl"": [{""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 5, ""gene_symbol"": ""ENSG00000258028"", ""hgvs_c"": ""n.154-8657_154-8634delCAAGAATATTAGTAGAAGCAGAAA"", ""transcript"": ""ENST00000652140.1"", ""cds_start"": -4, ""cdna_length"": 2873}, {""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 7, ""gene_symbol"": ""ENSG00000257522"", ""hgvs_c"": ""n.840+15916_840+15939delTTTCTGCTTCTACTAATATTCTTG"", ""transcript"": ""ENST00000652247.1"", ""cds_start"": -4, ""cdna_length"": 1231}], ""gene_symbol"": ""ENSG00000258028"", ""phylop100way_score"": 1.0, ""acmg_score"": 2, ""acmg_classification"": ""Uncertain_significance"", ""acmg_criteria"": ""PM2""}]}" +NM_005249.5(FOXG1):c.209_235del,BA1;BS2;BP3,PM1;PM2;BP3;BP7,1.20939469337463,BP3,BA1;BS2,PM1;PM2;BP7,,0,,,,PM2,0.251307964324951,,PM2,BA1;BP3;BS2,"The allele frequency of the c.209_235del variant in FOXG1 is 0.17% in Ashkenazi Jewish sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions BA1). The p.Gln70_Pro78del variant is observed in at least 2 unaffected individuals (GeneDx internal database) (BS2). The p.Gln70_Pro78del variant is an in-frame deletion present in a repetitive region of FOXG1 (BP3). In summary, the p.Gln70_Pro78del variant in FOXG1 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP3).","{'pvs1': {'name': 'PVS1', 'prediction': , 'summary': '', 'description': 'PVS1 prediction failed.'}, 'ps1': {'name': 'PS1', 'prediction': , 'summary': 'Error occurred during PS1/PM5 prediction. Error: No valid primary variant information for PS1/PM5 prediction.', 'description': ''}, 'ps2': {'name': 'PS2', 'prediction': , 'summary': '', 'description': ''}, 'ps3': {'name': 'PS3', 'prediction': , 'summary': '', 'description': ''}, 'ps4': {'name': 'PS4', 'prediction': , 'summary': '', 'description': ''}, 'pm1': {'name': 'PM1', 'prediction': , 'summary': 'Counting pathogenic variants in the range of 50bp.The range is 29236652 - 29236702. => \nFound 5 Pathogenic variants. => \nFound 4 or more pathogenic variants. PM1 is met.', 'description': ''}, 'pm2': {'name': 'PM2', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAllele frequency: 0.0001662339927861467.\nAllele frequency <= 1%: PM2 is met.Check zygosity.\n', 'description': ''}, 'pm3': {'name': 'PM3', 'prediction': , 'summary': '', 'description': ''}, 'pm4': {'name': 'PM4', 'prediction': , 'summary': 'Check consequences of the variant for PM4.\nVariant consequence is in-frame deletion/insertion.\nCheck if the variant is in a repeat region.\nVariant is not in a repeat region.\nVariant is not in a repeat region or a conserved domain. PM4 is met.', 'description': ''}, 'pm5': {'name': 'PM5', 'prediction': , 'summary': 'Error occurred during PS1/PM5 prediction. Error: No valid primary variant information for PS1/PM5 prediction.', 'description': ''}, 'pm6': {'name': 'PM6', 'prediction': , 'summary': '', 'description': ''}, 'pp1': {'name': 'PP1', 'prediction': , 'summary': '', 'description': ''}, 'pp2': {'name': 'PP2', 'prediction': , 'summary': 'Fetching transcript data. => \nError occurred during PP2 and BP1 prediction. Error: Transcript data is not fully set. Cannot initialize the PVS1 class.', 'description': ''}, 'pp3': {'name': 'PP3', 'prediction': , 'summary': 'Checking Scores. => \nAn error occurred during prediction. Error: Missing dbNSFP data.', 'description': ''}, 'pp4': {'name': 'PP4', 'prediction': , 'summary': '', 'description': ''}, 'pp5': {'name': 'PP5', 'prediction': , 'summary': '', 'description': ''}, 'ba1': {'name': 'BA1', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAllele frequency: 0.0001662339927861467.\nAllele frequency <= 1%: PM2 is met.Check zygosity.\n', 'description': ''}, 'bs1': {'name': 'BS1', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAllele frequency: 0.0001662339927861467.\nAllele frequency <= 1%: PM2 is met.Check zygosity.\n', 'description': ''}, 'bs2': {'name': 'BS2', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAllele frequency: 0.0001662339927861467.\nAllele frequency <= 1%: PM2 is met.Check zygosity.\n', 'description': ''}, 'bs3': {'name': 'BS3', 'prediction': , 'summary': '', 'description': ''}, 'bs4': {'name': 'BS4', 'prediction': , 'summary': '', 'description': ''}, 'bp1': {'name': 'BP1', 'prediction': , 'summary': '', 'description': ''}, 'bp2': {'name': 'BP2', 'prediction': , 'summary': '', 'description': ''}, 'bp3': {'name': 'BP3', 'prediction': , 'summary': 'Check consequences of the variant for PM4.\nVariant consequence is in-frame deletion/insertion.\nCheck if the variant is in a repeat region.\nVariant is not in a repeat region.\nVariant is not in a repeat region or a conserved domain. PM4 is met.', 'description': ''}, 'bp4': {'name': 'BP4', 'prediction': , 'summary': 'Checking Scores. => \nAn error occurred during prediction. Error: Missing dbNSFP data.', 'description': ''}, 'bp5': {'name': 'BP5', 'prediction': , 'summary': '', 'description': ''}, 'bp6': {'name': 'BP6', 'prediction': , 'summary': '', 'description': ''}, 'bp7': {'name': 'BP7', 'prediction': , 'summary': 'Checking for pathogenic variants in the range of 2bp. => \nNo pathogenic variants found in the range of 2bp. => \nChecking for proximity to splice site. => \nVariant is not within 2bp of a splice site. => \nPredicting splice site alterations using SpliceAI. => \nVariant is not a splice site alteration. BP7 is met.', 'description': ''}}",,"{""variants"": [{""chr"": ""14"", ""pos"": 29236677, ""ref"": ""CCTCAAGAATATTAGTAGAAGCAGAAAA"", ""alt"": ""C"", ""transcript"": ""ENST00000652140.1"", ""consequences_refseq"": [{""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 7, ""gene_symbol"": ""LOC102724934"", ""hgvs_c"": ""n.766-25290_766-25264delTTTTCTGCTTCTACTAATATTCTTGAG"", ""transcript"": ""XR_001750707.2"", ""cds_start"": -4, ""cdna_length"": 1057}, {""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 4, ""gene_symbol"": ""LOC102724934"", ""hgvs_c"": ""n.1054-25290_1054-25264delTTTTCTGCTTCTACTAATATTCTTGAG"", ""transcript"": ""XR_007064104.1"", ""cds_start"": -4, ""cdna_length"": 1482}], ""consequences_ensembl"": [{""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 5, ""gene_symbol"": ""ENSG00000258028"", ""hgvs_c"": ""n.154-8659_154-8633delCTCAAGAATATTAGTAGAAGCAGAAAA"", ""transcript"": ""ENST00000652140.1"", ""cds_start"": -4, ""cdna_length"": 2873}, {""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 7, ""gene_symbol"": ""ENSG00000257522"", ""hgvs_c"": ""n.840+15915_840+15941delTTTTCTGCTTCTACTAATATTCTTGAG"", ""transcript"": ""ENST00000652247.1"", ""cds_start"": -4, ""cdna_length"": 1231}], ""gene_symbol"": ""ENSG00000258028"", ""phylop100way_score"": 1.7419999837875366, ""acmg_score"": 2, ""acmg_classification"": ""Uncertain_significance"", ""acmg_criteria"": ""PM2""}]}" +NM_005249.5(FOXG1):c.237_239del,BA1;BP3,PM1,0.883777379989624,,BA1;BP3,PM1,,0,,,,PM2,0.254270315170288,,PM2,BA1;BP3,"The highest population minor allele frequency of the c.237_239del (p.Pro80del) variant in FOXG1 in gnomAD v4.1 is 0.00054 in the East Asian population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1). The p.Pro80del variant is an in-frame deletion present in a repetitive region of FOXG1 (BP3). In summary, the p.Pro80del variant in FOXG1 is classified as a benign variant based on the ACMG/AMP criteria (BA1, BP3).","{'pvs1': {'name': 'PVS1', 'prediction': , 'summary': '', 'description': 'PVS1 prediction failed.'}, 'ps1': {'name': 'PS1', 'prediction': , 'summary': 'Error occurred during PS1/PM5 prediction. Error: No valid primary variant information for PS1/PM5 prediction.', 'description': ''}, 'ps2': {'name': 'PS2', 'prediction': , 'summary': '', 'description': ''}, 'ps3': {'name': 'PS3', 'prediction': , 'summary': '', 'description': ''}, 'ps4': {'name': 'PS4', 'prediction': , 'summary': '', 'description': ''}, 'pm1': {'name': 'PM1', 'prediction': , 'summary': 'Counting pathogenic variants in the range of 50bp.The range is 29236694 - 29236744. => \nFound 14 Pathogenic variants. => \nFound 4 or more pathogenic variants. PM1 is met.', 'description': ''}, 'pm2': {'name': 'PM2', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAn error occurred while predicting BA1, BS1, BS2, PM2 criteria: No allele counts found in variant data', 'description': ''}, 'pm3': {'name': 'PM3', 'prediction': , 'summary': '', 'description': ''}, 'pm4': {'name': 'PM4', 'prediction': , 'summary': 'Check consequences of the variant for PM4.\nVariant consequence is not indel or stop-loss. PM4 and BP3 are not met.Check if the variant is in a repeat region.\nVariant is not in a repeat region.\n', 'description': ''}, 'pm5': {'name': 'PM5', 'prediction': , 'summary': 'Error occurred during PS1/PM5 prediction. Error: No valid primary variant information for PS1/PM5 prediction.', 'description': ''}, 'pm6': {'name': 'PM6', 'prediction': , 'summary': '', 'description': ''}, 'pp1': {'name': 'PP1', 'prediction': , 'summary': '', 'description': ''}, 'pp2': {'name': 'PP2', 'prediction': , 'summary': 'Fetching transcript data. => \nError occurred during PP2 and BP1 prediction. Error: Transcript data is not fully set. Cannot initialize the PVS1 class.', 'description': ''}, 'pp3': {'name': 'PP3', 'prediction': , 'summary': 'Checking Scores. => \nAn error occurred during prediction. Error: Missing dbNSFP data.', 'description': ''}, 'pp4': {'name': 'PP4', 'prediction': , 'summary': '', 'description': ''}, 'pp5': {'name': 'PP5', 'prediction': , 'summary': '', 'description': ''}, 'ba1': {'name': 'BA1', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAn error occurred while predicting BA1, BS1, BS2, PM2 criteria: No allele counts found in variant data', 'description': ''}, 'bs1': {'name': 'BS1', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAn error occurred while predicting BA1, BS1, BS2, PM2 criteria: No allele counts found in variant data', 'description': ''}, 'bs2': {'name': 'BS2', 'prediction': , 'summary': 'Check allele frequency for the control population.\nAn error occurred while predicting BA1, BS1, BS2, PM2 criteria: No allele counts found in variant data', 'description': ''}, 'bs3': {'name': 'BS3', 'prediction': , 'summary': '', 'description': ''}, 'bs4': {'name': 'BS4', 'prediction': , 'summary': '', 'description': ''}, 'bp1': {'name': 'BP1', 'prediction': , 'summary': '', 'description': ''}, 'bp2': {'name': 'BP2', 'prediction': , 'summary': '', 'description': ''}, 'bp3': {'name': 'BP3', 'prediction': , 'summary': 'Check consequences of the variant for PM4.\nVariant consequence is not indel or stop-loss. PM4 and BP3 are not met.Check if the variant is in a repeat region.\nVariant is not in a repeat region.\n', 'description': ''}, 'bp4': {'name': 'BP4', 'prediction': , 'summary': 'Checking Scores. => \nAn error occurred during prediction. Error: Missing dbNSFP data.', 'description': ''}, 'bp5': {'name': 'BP5', 'prediction': , 'summary': '', 'description': ''}, 'bp6': {'name': 'BP6', 'prediction': , 'summary': '', 'description': ''}, 'bp7': {'name': 'BP7', 'prediction': , 'summary': 'Checking for pathogenic variants in the range of 2bp. => \nFound pathogenic variants in the range of 2bp. BP7 is not met.', 'description': ''}}",,"{""variants"": [{""chr"": ""14"", ""pos"": 29236719, ""ref"": ""TTAC"", ""alt"": ""T"", ""transcript"": ""ENST00000652140.1"", ""consequences_refseq"": [{""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 7, ""gene_symbol"": ""LOC102724934"", ""hgvs_c"": ""n.766-25308_766-25306delGTA"", ""transcript"": ""XR_001750707.2"", ""cds_start"": -4, ""cdna_length"": 1057}, {""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 4, ""gene_symbol"": ""LOC102724934"", ""hgvs_c"": ""n.1054-25308_1054-25306delGTA"", ""transcript"": ""XR_007064104.1"", ""cds_start"": -4, ""cdna_length"": 1482}], ""consequences_ensembl"": [{""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 5, ""gene_symbol"": ""ENSG00000258028"", ""hgvs_c"": ""n.154-8617_154-8615delTAC"", ""transcript"": ""ENST00000652140.1"", ""cds_start"": -4, ""cdna_length"": 2873}, {""protein_coding"": false, ""consequences"": [""intron_variant""], ""exon_count"": 7, ""gene_symbol"": ""ENSG00000257522"", ""hgvs_c"": ""n.840+15897_840+15899delGTA"", ""transcript"": ""ENST00000652247.1"", ""cds_start"": -4, ""cdna_length"": 1231}], ""gene_symbol"": ""ENSG00000258028"", ""phylop100way_score"": 0.6060000061988831, ""acmg_score"": 2, ""acmg_classification"": ""Uncertain_significance"", ""acmg_criteria"": ""PM2""}]}" diff --git a/src/bench/results_analysis.ipynb b/src/bench/results_analysis_v1.ipynb similarity index 100% rename from src/bench/results_analysis.ipynb rename to src/bench/results_analysis_v1.ipynb diff --git a/src/bench/results_analysis_v2.ipynb b/src/bench/results_analysis_v2.ipynb new file mode 100644 index 0000000..ea32e41 --- /dev/null +++ b/src/bench/results_analysis_v2.ipynb @@ -0,0 +1,777 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 22, + "id": "24750acd", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import matplotlib.pyplot as plt\n", + "import os\n", + "from sklearn.metrics import cohen_kappa_score\n", + "from scipy.stats import pearsonr\n", + "import seaborn as sns" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "id": "4932e000", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Path: /home/gromdimon/Working/auto-acmg/src/bench/results.csv\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/tmp/ipykernel_322321/2337496807.py:6: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.\n", + " df.fillna('', inplace=True)\n" + ] + }, + { + "data": { + "text/html": [ + "
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VariantExpected CriteriaAutoACMG CriteriaAutoACMG Prediction timeAutoACMG True PositivesAutoACMG False NegativesAutoACMG False PositivesIntervar CriteriaIntervar Prediction timeIntervar True Positives...Intervar False PositivesGenebe CriteriaGenebe Prediction timeGenebe True PositivesGenebe False PositivesGenebe False NegativesCommentUnnamed: 18Unnamed: 19Unnamed: 20
04-113568536-G-GAPVS1PVS1;PM1;PM23.329291PVS1PM1;PM20.0...0.268924PVS1Gene: LARP7
1NM_004360.3:c.1085delTPVS1PVS1;PM11.597754PVS1PM10.0...PVS1;PS4;PM2;PM50.307956PVS1PS4;PM5;PM2Gene: CDH1; p.Val362GlyfsTer31; From Recommend...
2NM_000152.4:c.525delTPVS1PVS1;PM1;PM21.649675PVS1PM1;PM20.0...PVS1;PM2;PM3;PP40.361843PVS1PM3;PP4;PM2Gene: GAA; p.Glu176ArgfsTer45; From Recommenda...
3NM_000152.4:c.1987delCPVS1PVS1;PM11.531021PVS1PM10.0...PVS1;PM2;PP50.339899PVS1PP5;PM2Gene: GAA; p.Gln663SerfsTer33; From Recommenda...
4NM_000152.4:c.2706delGPVS1PVS1;PM11.397128PVS1PM10.0...PVS1;PM2;PM3;PP40.344012PVS1PM3;PP4;PM2Gene: GAA; p.Lys903ArgfsTer2; From Recommendat...
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" + ], + "text/plain": [ + " Variant Expected Criteria AutoACMG Criteria \\\n", + "0 4-113568536-G-GA PVS1 PVS1;PM1;PM2 \n", + "1 NM_004360.3:c.1085delT PVS1 PVS1;PM1 \n", + "2 NM_000152.4:c.525delT PVS1 PVS1;PM1;PM2 \n", + "3 NM_000152.4:c.1987delC PVS1 PVS1;PM1 \n", + "4 NM_000152.4:c.2706delG PVS1 PVS1;PM1 \n", + "\n", + " AutoACMG Prediction time AutoACMG True Positives AutoACMG False Negatives \\\n", + "0 3.329291 PVS1 PM1;PM2 \n", + "1 1.597754 PVS1 PM1 \n", + "2 1.649675 PVS1 PM1;PM2 \n", + "3 1.531021 PVS1 PM1 \n", + "4 1.397128 PVS1 PM1 \n", + "\n", + " AutoACMG False Positives Intervar Criteria Intervar Prediction time \\\n", + "0 0.0 \n", + "1 0.0 \n", + "2 0.0 \n", + "3 0.0 \n", + "4 0.0 \n", + "\n", + " Intervar True Positives ... Intervar False Positives Genebe Criteria \\\n", + "0 ... \n", + "1 ... PVS1;PS4;PM2;PM5 \n", + "2 ... PVS1;PM2;PM3;PP4 \n", + "3 ... PVS1;PM2;PP5 \n", + "4 ... PVS1;PM2;PM3;PP4 \n", + "\n", + " Genebe Prediction time Genebe True Positives Genebe False Positives \\\n", + "0 0.268924 \n", + "1 0.307956 PVS1 PS4;PM5;PM2 \n", + "2 0.361843 PVS1 PM3;PP4;PM2 \n", + "3 0.339899 PVS1 PP5;PM2 \n", + "4 0.344012 PVS1 PM3;PP4;PM2 \n", + "\n", + " Genebe False Negatives Comment \\\n", + "0 PVS1 Gene: LARP7 \n", + "1 Gene: CDH1; p.Val362GlyfsTer31; From Recommend... \n", + "2 Gene: GAA; p.Glu176ArgfsTer45; From Recommenda... \n", + "3 Gene: GAA; p.Gln663SerfsTer33; From Recommenda... \n", + "4 Gene: GAA; p.Lys903ArgfsTer2; From Recommendat... \n", + "\n", + " Unnamed: 18 Unnamed: 19 Unnamed: 20 \n", + "0 \n", + "1 \n", + "2 \n", + "3 \n", + "4 \n", + "\n", + "[5 rows x 21 columns]" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Load the CSV file\n", + "path_to_csv = os.path.join(os.path.abspath(''), 'src', 'bench', 'results.csv')\n", + "print(f\"Path: {path_to_csv}\")\n", + "df = pd.read_csv(path_to_csv)\n", + "# Replace NaN values with empty strings\n", + "df.fillna('', inplace=True)\n", + "\n", + "df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "c4748cb6-5950-4499-919c-8df0191cfc80", + "metadata": {}, + "outputs": [], + "source": [ + "# Define the criteria and not_implemented lists\n", + "criteria = [\n", + " \"PVS1\", \"PS1\", \"PS2\", \"PS3\", \"PS4\", \"PM1\", \"PM2\", \"PM3\", \"PM4\", \"PM5\", \"PM6\",\n", + " \"PP1\", \"PP2\", \"PP3\", \"PP4\", \"PP5\", \"BA1\", \"BS1\", \"BS2\", \"BS3\", \"BS4\",\n", + " \"BP1\", \"BP2\", \"BP3\", \"BP4\", \"BP5\", \"BP6\", \"BP7\"\n", + "]\n", + "\n", + "not_implemented = [\n", + " \"PS2\", \"PS3\", \"PS4\", \"PM3\", \"PM6\", \"PP1\", \"PP4\", \"PP5\", \"BS3\", \"BS4\", \"BP2\", \"BP5\", \"BP6\"\n", + "]\n", + "\n", + "# Function to compute Cohen's Kappa for each criterion\n", + "def compute_kappa(df, criteria):\n", + " kappa_results = {\n", + " \"Criteria\": [],\n", + " \"AutoACMG Kappa\": [],\n", + " \"Intervar Kappa\": [],\n", + " \"Genebe Kappa\": []\n", + " }\n", + "\n", + " for c in criteria:\n", + " if c in not_implemented:\n", + " continue\n", + "\n", + " expected = df[\"Expected Criteria\"].apply(lambda x: 1 if c in x else 0)\n", + " autoacmg = df[\"AutoACMG Criteria\"].apply(lambda x: 1 if c in x else 0)\n", + " intervar = df[\"Intervar Criteria\"].apply(lambda x: 1 if c in x else 0)\n", + " genebe = df[\"Genebe Criteria\"].apply(lambda x: 1 if c in x else 0)\n", + "\n", + " kappa_results[\"Criteria\"].append(c)\n", + " kappa_results[\"AutoACMG Kappa\"].append(cohen_kappa_score(expected, autoacmg))\n", + " kappa_results[\"Intervar Kappa\"].append(cohen_kappa_score(expected, intervar))\n", + " kappa_results[\"Genebe Kappa\"].append(cohen_kappa_score(expected, genebe))\n", + "\n", + " return pd.DataFrame(kappa_results)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "c9956608-aefa-4386-9096-c2edcbdcd8b9", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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CriteriaAutoACMG KappaIntervar KappaGenebe Kappa
0PVS10.9059420.2349020.952971
1PS10.3481650.0000000.708042
2PM1-0.0058150.3281370.610023
3PM2-0.3840760.5030120.540544
4PM41.0000000.0000000.660569
5PM50.6311550.1009840.675432
6PP20.000000-0.0655670.806282
7PP30.2832620.5914590.754988
8BA10.0000000.1009840.756264
9BS1-0.011178-0.0609910.583125
10BS2-0.0115880.1019950.492888
11BP10.0000000.3423210.926754
12BP30.7970840.0000000.000000
13BP4-0.2011300.6171480.932725
14BP70.7277470.7874160.912915
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" + ], + "text/plain": [ + " Criteria AutoACMG Kappa Intervar Kappa Genebe Kappa\n", + "0 PVS1 0.905942 0.234902 0.952971\n", + "1 PS1 0.348165 0.000000 0.708042\n", + "2 PM1 -0.005815 0.328137 0.610023\n", + "3 PM2 -0.384076 0.503012 0.540544\n", + "4 PM4 1.000000 0.000000 0.660569\n", + "5 PM5 0.631155 0.100984 0.675432\n", + "6 PP2 0.000000 -0.065567 0.806282\n", + "7 PP3 0.283262 0.591459 0.754988\n", + "8 BA1 0.000000 0.100984 0.756264\n", + "9 BS1 -0.011178 -0.060991 0.583125\n", + "10 BS2 -0.011588 0.101995 0.492888\n", + "11 BP1 0.000000 0.342321 0.926754\n", + "12 BP3 0.797084 0.000000 0.000000\n", + "13 BP4 -0.201130 0.617148 0.932725\n", + "14 BP7 0.727747 0.787416 0.912915" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Compute Cohen's Kappa for the criteria\n", + "kappa_df = compute_kappa(df, criteria)\n", + "display(kappa_df)\n", + "\n", + "# Export the results to a CSV file\n", + "kappa_df.to_csv(\"cohens_kappa_results.csv\", index=False)" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "id": "d3cd8e0c-20e8-4c51-acb5-6810c4697b25", + "metadata": {}, + "outputs": [], + "source": [ + "very_strong = [\"PVS1\"]\n", + "strong = [\"PS1\", \"PS2\", \"PS3\", \"PS4\"]\n", + "moderate = [\"PM1\", \"PM2\", \"PM3\", \"PM4\", \"PM5\", \"PM6\"]\n", + "supporting = [\"PP1\", \"PP2\", \"PP3\", \"PP4\", \"PP5\"]\n", + "stand_alone = [\"BA1\"]\n", + "strong_benign = [\"BS1\", \"BS2\", \"BS3\", \"BS4\"]\n", + "supporting_benign = [\"BP1\", \"BP2\", \"BP3\", \"BP4\", \"BP5\", \"BP6\", \"BP7\"]\n", + "\n", + "def classify_variant(criteria_list):\n", + " very_strong_count = len([c for c in criteria_list if c in very_strong])\n", + " strong_count = len([c for c in criteria_list if c in strong])\n", + " moderate_count = len([c for c in criteria_list if c in moderate])\n", + " supporting_count = len([c for c in criteria_list if c in supporting])\n", + " stand_alone_count = len([c for c in criteria_list if c in stand_alone])\n", + " strong_benign_count = len([c for c in criteria_list if c in strong_benign])\n", + " supporting_benign_count = len([c for c in criteria_list if c in supporting_benign])\n", + " \n", + " # Pathogenic\n", + " if (\n", + " (very_strong_count >= 1 and (strong_count >= 1 or moderate_count >= 2 or (moderate_count >= 1 and supporting_count >= 1) or supporting_count >= 2)) or\n", + " (strong_count >= 2 or (strong_count >= 1 and moderate_count >= 3) or (moderate_count >= 2 and supporting_count >= 2) or (moderate_count >= 1 and supporting_count >= 4))\n", + " ):\n", + " return 2 # Pathogenic\n", + " \n", + " # Likely Pathogenic\n", + " if (\n", + " (very_strong_count >= 1 and moderate_count >= 1) or\n", + " (strong_count >= 1 and 1 <= moderate_count <= 2) or\n", + " (strong_count >= 1 and supporting_count >= 2) or\n", + " (moderate_count >= 3) or\n", + " (moderate_count >= 2 and supporting_count >= 2) or\n", + " (moderate_count >= 1 and supporting_count >= 4)\n", + " ):\n", + " return 1 # Likely Pathogenic\n", + " \n", + " # Benign\n", + " if (stand_alone_count >= 1 or strong_benign_count >= 2):\n", + " return -2 # Benign\n", + " \n", + " # Likely Benign\n", + " if (strong_benign_count >= 1 and supporting_benign_count >= 1) or (supporting_benign_count >= 2):\n", + " return -1 # Likely Benign\n", + " \n", + " return 0 # Uncertain Significance\n" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "1b2e1208-8f72-421c-8aa4-7c86fb98c1f0", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " Variant Expected Criteria AutoACMG Criteria \\\n", + "0 4-113568536-G-GA PVS1 PVS1;PM1;PM2 \n", + "1 NM_004360.3:c.1085delT PVS1 PVS1;PM1 \n", + "2 NM_000152.4:c.525delT PVS1 PVS1;PM1;PM2 \n", + "3 NM_000152.4:c.1987delC PVS1 PVS1;PM1 \n", + "4 NM_000152.4:c.2706delG PVS1 PVS1;PM1 \n", + ".. ... ... ... \n", + "162 NM_000546.5(TP53):c.869G>A BS1;BS2;BS3;BP4 PM1;PM2 \n", + "163 NM_000441.2(SLC26A4):c.1708-18T>A BA1;BP4;BP7 PM1;BS1;BS2 \n", + "164 NM_005249.4(FOXG1):c.209_232del24 BA1;BS2;BP3;BP5 PM1;PM2;BP3;BP7 \n", + "165 NM_005249.5(FOXG1):c.209_235del BA1;BS2;BP3 PM1;PM2;BP3;BP7 \n", + "166 NM_005249.5(FOXG1):c.237_239del BA1;BP3 PM1 \n", + "\n", + " AutoACMG Prediction time AutoACMG True Positives \\\n", + "0 3.329291 PVS1 \n", + "1 1.597754 PVS1 \n", + "2 1.649675 PVS1 \n", + "3 1.531021 PVS1 \n", + "4 1.397128 PVS1 \n", + ".. ... ... \n", + "162 1062.644831 BP4;BS1 \n", + "163 2.561002 BP7;BA1 \n", + "164 1.160095 BP3 \n", + "165 1.209395 BP3 \n", + "166 0.883777 \n", + "\n", + " AutoACMG False Negatives AutoACMG False Positives Intervar Criteria \\\n", + "0 PM1;PM2 \n", + "1 PM1 \n", + "2 PM1;PM2 \n", + "3 PM1 \n", + "4 PM1 \n", + ".. ... ... ... \n", + "162 PM1;PM2 BS3;BS2 PM1;PM2;BP6;BS2 \n", + "163 PM1;BS1;BS2 \n", + "164 BA1;BP5;BS2 PM1;PM2;BP7 \n", + "165 BA1;BS2 PM1;PM2;BP7 \n", + "166 BA1;BP3 PM1 \n", + "\n", + " Intervar Prediction time Intervar True Positives ... Unnamed: 19 \\\n", + "0 0.000000 ... \n", + "1 0.000000 ... \n", + "2 0.000000 ... \n", + "3 0.000000 ... \n", + "4 0.000000 ... \n", + ".. ... ... ... ... \n", + "162 0.402278 BS2 ... \n", + "163 0.000000 ... \n", + "164 0.000000 ... \n", + "165 0.000000 ... \n", + "166 0.000000 ... \n", + "\n", + " Unnamed: 20 AutoACMG Criteria List \\\n", + "0 [PVS1, PM1, PM2] \n", + "1 [PVS1, PM1] \n", + "2 [PVS1, PM1, PM2] \n", + "3 [PVS1, PM1] \n", + "4 [PVS1, PM1] \n", + ".. ... ... \n", + "162 [PM1, PM2] \n", + "163 [PM1, BS1, BS2] \n", + "164 {\"variants\": [{\"chr\": \"14\", \"pos\": 29236679, \"... [PM1, PM2, BP3, BP7] \n", + "165 {\"variants\": [{\"chr\": \"14\", \"pos\": 29236677, \"... [PM1, PM2, BP3, BP7] \n", + "166 {\"variants\": [{\"chr\": \"14\", \"pos\": 29236719, \"... [PM1] \n", + "\n", + " Intervar Criteria List Genebe Criteria List Expected Criteria List \\\n", + "0 [] [] [PVS1] \n", + "1 [] [PVS1, PS4, PM2, PM5] [PVS1] \n", + "2 [] [PVS1, PM2, PM3, PP4] [PVS1] \n", + "3 [] [PVS1, PM2, PP5] [PVS1] \n", + "4 [] [PVS1, PM2, PM3, PP4] [PVS1] \n", + ".. ... ... ... \n", + "162 [PM1, PM2, BP6, BS2] [BS1, BS2, BS3, BP4] [BS1, BS2, BS3, BP4] \n", + "163 [] [BA1, BP4, BP7] [BA1, BP4, BP7] \n", + "164 [] [PM2] [BA1, BS2, BP3, BP5] \n", + "165 [] [PM2] [BA1, BS2, BP3] \n", + "166 [] [PM2] [BA1, BP3] \n", + "\n", + " AutoACMG_Score Intervar_Score Genebe_Score ClinGen_Score \n", + "0 2 0 0 0 \n", + "1 1 0 2 0 \n", + "2 2 0 2 0 \n", + "3 1 0 2 0 \n", + "4 1 0 2 0 \n", + ".. ... ... ... ... \n", + "162 0 -1 -2 -2 \n", + "163 -2 0 -2 -2 \n", + "164 -1 0 0 -2 \n", + "165 -1 0 0 -2 \n", + "166 0 0 0 -2 \n", + "\n", + "[167 rows x 29 columns]\n" + ] + } + ], + "source": [ + "# Define a function to split criteria strings into lists\n", + "def split_criteria(criteria_str):\n", + " if pd.isna(criteria_str) or criteria_str == '':\n", + " return []\n", + " return criteria_str.split(';')\n", + "\n", + "# Apply the function to create lists of criteria\n", + "df['AutoACMG Criteria List'] = df['AutoACMG Criteria'].apply(split_criteria)\n", + "df['Intervar Criteria List'] = df['Intervar Criteria'].apply(split_criteria)\n", + "df['Genebe Criteria List'] = df['Genebe Criteria'].apply(split_criteria)\n", + "df['Expected Criteria List'] = df['Expected Criteria'].apply(split_criteria)\n", + "\n", + "# Apply the classification function to each list of criteria\n", + "df['AutoACMG_Score'] = df['AutoACMG Criteria List'].apply(classify_variant)\n", + "df['Intervar_Score'] = df['Intervar Criteria List'].apply(classify_variant)\n", + "df['Genebe_Score'] = df['Genebe Criteria List'].apply(classify_variant)\n", + "df['ClinGen_Score'] = df['Expected Criteria List'].apply(classify_variant)\n", + "\n", + "# Display the updated DataFrame\n", + "print(df)\n", + "\n", + "# Save the updated DataFrame to a CSV file\n", + "df.to_csv(\"updated_results_with_classification_scores.csv\", index=False)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "id": "a7e8e8e6-c63a-4bb4-ac4b-84a357614b90", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " AutoACMG Intervar Genebe ClinGen\n", + "AutoACMG 1.000000 0.008763 0.288313 0.119735\n", + "Intervar 0.008763 1.000000 0.672919 0.796525\n", + "Genebe 0.288313 0.672919 1.000000 0.800186\n", + "ClinGen 0.119735 0.796525 0.800186 1.000000\n" + ] + }, + { + "data": { + "image/png": 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/7x17hIaGavr06dbJ8ZUqVco0pv++586fP6+4uDh9+umnWd597Ny5c9b4KlasmOFDf2bvj/86cuSIQkJCbJLRW5HVe9PNzU3h4eEZrmWZMmUyxO3n56c9e/bc9LXc3d01dOhQDR06VGfPntWPP/6ojz76SAsWLJCrq6u++OILnT9/XgkJCapevfpN465fv36G9n+/B/59jFv5GfH++++rc+fOKlu2rOrUqaOWLVuqU6dOCg8Pv+k5A0BuIInAbc3b21shISHau3evXftl99vTzO7ElNVz179BHDduXJa3Ic1q/kJcXJwaN24sb29vjR49WhUqVJCHh4d27typQYMGOWy9gKzuoGP8b+Jwdri7u+vxxx/X7NmzdfToUY0cOTLLvu+8846GDRumbt26acyYMfL395fZbFbfvn3tOucb/Ttl5vfff7d+uP7jjz/09NNP27V/bvPy8lJkZORN+2X1nnv22Wez/GBao0aNWw8wn+XG+1KSgoOD1aFDB7Vr107VqlXTggUL8nRxxlv5GfHUU0/pvvvu05IlS7R69WqNGzdO7733nhYvXnzDeSAAkFtIInDbe+SRR/Tpp59qy5YtatCgwQ37li9fXhaLRYcOHbKZ7BodHa24uDjrRMycuD6J1NvbO1sfCP9t48aNunjxohYvXqz777/f2n7s2LEMfbObAF0/l4MHD2Z47sCBAypZsqRNFSI3PfPMM5oxY4bMZrM6dOiQZb+FCxeqSZMm+vzzz23a4+LiVLJkSevjnAyZyUpSUpK6du2qiIgINWzYUO+//74ee+wx6x2gslK+fHmtXbtWiYmJNtWI60PNbuW9k1MBAQEqXry40tPTb/qeK1++vPbu3SvDMGyuZ2bvj/+qUKGCVq1apZiYmBtWI3Ly3vz3N+tXr17VsWPH7P7/Yy9XV1fVqFFDhw4d0oULF1SqVCl5e3vf9MuI8uXLZ/n/6frzN2Lvz4jg4GC99NJLeumll3Tu3Dndddddevvtt0kiADgEcyJw2xs4cKC8vLz0/PPPKzo6OsPzR44c0UcffSTp2lAbSRlWfJ4wYYIkqVWrVjmOo06dOqpQoYLGjx+vS5cuZXj++q06M3P9m9Z/f7N69epVTZs2LUNfLy+vbA1vCg4OVq1atTR79myb22bu3btXq1evtl6LvNCkSRONGTNGU6ZMUVBQUJb9XFxcMnyb/M033+j06dM2bdeTndy4r/+gQYN08uRJzZ49WxMmTFBoaKg6d+6c6a1O/61ly5ZKT0/XlClTbNo//PBDmUymfPlg5+Lionbt2mnRokWZfgD+93uuZcuWOnPmjBYuXGhtu3z5crYWYWzXrp0Mw9CoUaMyPPfvfz8vL69s/RtFRkbKzc1NkyZNstn/888/V3x8/C39P/y3Q4cO6eTJkxna4+LitGXLFvn5+SkgIEBms1lt27bVsmXLrLes/bfrMbZs2VLbtm3Tli1brM8lJSXp008/VWhoqM18lcxk92dEenp6hv/jpUqVUkhIyE3fpwCQW6hE4LZXoUIFzZs3T+3bt1fVqlVtVqz+5Zdf9M0331jvV1+zZk117txZn376qXUI0bZt2zR79my1bdtWTZo0yXEcZrNZn332mVq0aKFq1aqpa9euKl26tE6fPq0NGzbI29tby5Yty3Tfhg0bys/PT507d1afPn1kMpk0d+7cTIdr1KlTR19//bX69++vu+++W8WKFVPr1q0zPe64cePUokULNWjQQN27d7fe4tXHx+eGw4xuldls1ptvvnnTfo888ohGjx6trl27qmHDhvrjjz/05ZdfZhj3XaFCBfn6+urjjz9W8eLF5eXlpfr1699wzkpm1q9fr2nTpmnEiBHW22TOnDlTDzzwgIYNG3bDtQdat26tJk2aaOjQoTp+/Lhq1qyp1atX69tvv1Xfvn1veDvTvPTuu+9qw4YNql+/vnr06KGIiAjFxMRo586dWrt2rWJiYiRdm7Q8ZcoUderUSTt27FBwcLDmzp0rT0/Pm75GkyZN9Nxzz2nSpEk6dOiQmjdvLovFos2bN6tJkybq3bu3pGvvzbVr12rChAkKCQlRWFhYpnMIAgICNGTIEI0aNUrNmzdXmzZtdPDgQU2bNk133323zSTqW7F7924988wzatGihe677z75+/vr9OnTmj17ts6cOaOJEydaE/h33nlHq1evVuPGjdWzZ09VrVpVZ8+e1TfffKOffvpJvr6+Gjx4sL766iu1aNFCffr0kb+/v2bPnq1jx45p0aJFN11ILrs/IxITE1WmTBk98cQTqlmzpooVK6a1a9dq+/bt+uCDD3Ll2gDATeXLPaGAfPDXX38ZPXr0MEJDQw03NzejePHiRqNGjYzJkyfb3CI1NTXVGDVqlBEWFma4uroaZcuWNYYMGWLTxzCu3eK1VatWGV7n+u0bv/nmm0zj+P33343HH3/cKFGihOHu7m6UL1/eeOqpp4x169ZZ+2R2i9eff/7ZuOeee4yiRYsaISEhxsCBA623I/337TcvXbpkPPPMM4avr68hyXorzsxu8WoYhrF27VqjUaNGRtGiRQ1vb2+jdevWxr59+2z6XL/F6/nz523aM4szM/++xWtWsrrF62uvvWYEBwcbRYsWNRo1amRs2bIl01uzfvvtt0ZERIRRpEgRm/O80e1U/32chIQEo3z58sZdd91lpKam2vTr16+fYTabjS1bttzwHBITE41+/foZISEhhqurq1GpUiVj3LhxNrfrvFlMmcWYnb6SsrzlZ3R0tPHyyy8bZcuWNVxdXY2goCCjadOmxqeffmrT78SJE0abNm0MT09Po2TJksarr75qrFy58qa3eDUMw0hLSzPGjRtnVKlSxXBzczMCAgKMFi1aGDt27LD2OXDggHH//fcbRYsWNSRZb/ea1ftoypQpRpUqVQxXV1cjMDDQ6NWrlxEbG5ut65NZjJldl3fffddo3LixERwcbBQpUsTw8/MzHnzwQWPhwoUZ+p84ccLo1KmTERAQYLi7uxvh4eHGyy+/bKSkpFj7HDlyxHjiiScMX19fw8PDw6hXr56xfPlym+Pc6s+IlJQU4/XXXzdq1qxpFC9e3PDy8jJq1qxpTJs27YbnCwC5yWQYds48AwAAAFCoMScCAAAAgF1IIgAAAADYhSQCAAAAgF1IIgAAAAAH2bRpk1q3bq2QkBCZTCYtXbr0pvts3LhRd911l9zd3VWxYsVMF8KcOnWqQkND5eHhofr162vbtm25H/y/kEQAAAAADpKUlKSaNWtq6tSp2ep/7NgxtWrVSk2aNNGuXbvUt29fPf/881q1apW1z/Vbu48YMUI7d+5UzZo11axZM507dy6vTkPcnQkAAADIByaTSUuWLFHbtm2z7DNo0CB9//33NouGdujQQXFxcVq5cqUkqX79+rr77rutC55aLBaVLVtWr7zyigYPHpwnsVOJAAAAAHIoJSVFCQkJNlturh6/ZcsWRUZG2rQ1a9ZMW7ZskSRdvXpVO3bssOljNpsVGRlp7ZMXCsyK1d+7Vs7vEFBIRBz4Pr9DQCER9Pf2/A4BhURSydD8DgGFRMnqDfI7hEzl5+fI7UOf1qhRo2zaRowYoZEjR+bK8aOiohQYGGjTFhgYqISEBF25ckWxsbFKT0/PtM+BAwdyJYbMFJgkAgAAAHA2Q4YMUf/+/W3a3N3d8ykaxyGJAAAAAHLI3d09T5OGoKAgRUdH27RFR0fL29tbRYsWlYuLi1xcXDLtExQUlGdxMScCAAAATs3kasq3La81aNBA69ats2lbs2aNGjS4NrTMzc1NderUseljsVi0bt06a5+8QBIBAAAAOMilS5e0a9cu7dq1S9K1W7ju2rVLJ0+elHRteFSnTp2s/V988UUdPXpUAwcO1IEDBzRt2jQtWLBA/fr1s/bp37+/pk+frtmzZ2v//v3q1auXkpKS1LVr1zw7D4YzAQAAwKmZi+R9RSC3/Pbbb2rSpIn18fX5FJ07d9asWbN09uxZa0IhSWFhYfr+++/Vr18/ffTRRypTpow+++wzNWvWzNqnffv2On/+vIYPH66oqCjVqlVLK1euzDDZOjcVmHUiuDsTHIW7M8FRuDsTHIW7M8FRCurdmVZ6V823126esD/fXjs/UYkAAACAUzO5MkLf0bjiAAAAAOxCEgEAAADALgxnAgAAgFNzponVtwsqEQAAAADsQiUCAAAATs0Ri77BFpUIAAAAAHYhiQAAAABgF4YzAQAAwKkxsdrxqEQAAAAAsAuVCAAAADg1JlY7HpUIAAAAAHYhiQAAAABgF4YzAQAAwKkxsdrxqEQAAAAAsAuVCAAAADg1kwuVCEejEgEAAADALlQiAAAA4NTMVCIcjkoEAAAAALuQRAAAAACwC8OZAAAA4NRMZoYzORqVCAAAAAB2oRIBAAAAp2Zy4XtxR+OKAwAAALALSQQAAAAAuzCcCQAAAE6NdSIcj0oEAAAAALtQiQAAAIBT4xavjkclAgAAAIBdqEQAAADAqTEnwvGoRAAAAACwC0kEAAAAALswnAkAAABOzcRwJoejEgEAAADALlQiAAAA4NRMZr4XdzSuOAAAAAC7ZLsScfbsWU2ZMkVvv/22JOnee+/V5cuXrc+7uLho6dKlKl26dO5HCQAAAKDAyHYlYtq0aYqNjbU+3r17t+677z49+uijevTRR+Xi4qIPP/wwT4IEAAAAsmIym/JtK6yyXYlYvny5Jk2aZNP26quvKjw8XJJ0zz33qH///ho/fnzuRggAAACgQMl2EnH8+HGFhYVZHz/00EPy8vKyPq5cubKOHTuWu9EBAAAAN8GK1Y6X7eFMqampOn/+vPXx4sWLFRgYaH0cGxsrMzPjAQAAgNtetj/1V65cWb/88kuWz2/evFl33HFHrgQFAAAAZBdzIhwv20lEhw4dNHz4cO3ZsyfDc7t379bo0aP19NNP52pwAAAAAAqebM+J6Nu3r5YvX646derooYceUuXKlSVJBw8e1Jo1a9SgQQP17ds3r+IEAAAAUEBkO4lwdXXVmjVrNGHCBM2fP18bN26UJFWqVEljxoxRv3795OrqmldxAgAAAJlixWrHy3YSIUlubm4aPHiwBg8enFfxAAAAACjg7EoiAAAAgIKmME9wzi/ZTiKuLyp3M0ePHs1xMAAAAAAKPrsWmytfvryeeeYZlSpVKi9jAgAAAFCAZTuJ+PrrrzVjxgxNmDBBLVq0ULdu3dSyZUsWmAMAAEC+YsVqx8t2BvDkk09qxYoVOnz4sOrUqaN+/fqpbNmyGjx4sA4dOpSXMQIAAAAoQOwuI5QuXVpDhw7VoUOHNG/ePG3dulVVqlRRbGxsXsQHAAAA3BArVjteju7OlJycrIULF2rGjBnaunWrnnzySXl6euZ2bAAAAAAKILuSiK1bt+rzzz/XggULFB4erm7dumnRokXy8/PLq/gAAACAG2KxOcfLdhJRrVo1nTt3Ts8884x+/PFH1axZMy/jAgAAAFBAZTuJ2L9/v7y8vDRnzhzNnTs3y34xMTG5EhgAAACAginbScTMmTPzMg4AAAAgRwrzBOf8ku0konPnznkZBwAAAAAnke1ZKLGxsZo8ebISEhIyPBcfH5/lcwAAAEBe4havjpftJGLKlCnatGmTvL29Mzzn4+OjzZs3a/LkybkaHAAAAICCJ9tJxKJFi/Tiiy9m+fwLL7yghQsX5kpQAAAAAAqubM+JOHLkiCpVqpTl85UqVdKRI0dyJSgAAAAguwrzsKL8ku1KhIuLi86cOZPl82fOnJGZhT4AAACA2162P/XXrl1bS5cuzfL5JUuWqHbt2rkREwAAAJBtJrM537bCKtvDmXr37q0OHTqoTJky6tWrl1xcXCRJ6enpmjZtmj788EPNmzcvzwLFNf731lX4a93lc1d1eYSU0m/tXlL0d+vyOywUIN8tW66FixYpNjZW4WFheqnXi6pcuXKW/Tdt3qw5c79QdHS0SoeEqFu3rqp3993W5w3D0NwvvtCKlauUlJSkiIiqeuXll1W6dGlrn1OnTuuzGZ9r3779SktNVWhYmDo/96zNyvYH//pLM2fO0qHDh2UySXfcUVnPd+uq8PDwvLkQKBDmb9im2Wt+1sX4S7qjTJAGdWihO8PKZNp30eYdWv7rbh0+c06SFFEuWL3bNrXpfzHhkiYuXqNf9x1R4uVk3VWpvAZ1aKnygSUccj4ouBatWKt5365QTFy8KoaWU7/uzyqiUuY/X46ePK3P5i/WwaPHFXX+ovp0fVrtH2lm02fO4uX68dcdOnH6rNzdXHVn5Yrq9dxTKl862BGnAxR42U6f2rVrp4EDB6pPnz7y9/dX7dq1Vbt2bfn7+6tv377q37+/nnjiibyMFZJcvDyVsOeg9vYZld+hoAD68cdNmj59up595hlNmTxJ4eFhGjpsmOLi4jLtv2/fPr373vtq9vDDmjp5kho0aKDRY97S8ePHrX2+WbhQ3363TH16v6yJH06Qh4eHhg4bpqtXr1r7jBg5Uunp6Xp37DuaPOkjhYeFafjIUdYV7K9cuaI3hw1XQECAJn44QePHjZNn0aIaOmyY0tLS8vKSIB+t2r5XHyxcpRdaPaCvhr6gO8oE6qVJXygm4VKm/X/767ia311d0/t31pxB3RXo56NeH81VdOy124cbhqF+0+br9PlYffjS05r/5osKLuGrFyfO0ZWUq5keE4XD2p+3avKs+er2VFvNGDdKFcuXVf8x4xUbn/mt51OupigkMEC9nn1SJXx9Mu2z688Derz5g/p07DBNHPG60tLT1W/0eF1JTsnLU0EOmV1M+bYVVnbVYN5++239+uuv6tKli0JCQhQcHKyuXbtqy5Ytevfdd/MqRvzL+VWb9NeIiYr+dm1+h4ICaPGSJWrevLkefvghlS9XTq/07i13dw+tWr060/5Lv/1OdevU0ZNPtFO5cuXUudNzqlihgr5btlzStQ9tS5Z+q6c7tFeDBg0UHham1197TRcvxuiXLVskXVsn5vSZM2r/5JMKDwtT6dKl1a1rF6WkpOj4iROSpL//PqXExER1eu5ZlS1TRqHly6vjM88oNjZO586dc8zFgcPNXbtFj997l9o2qq0KIaX0ZsdH5OHmqqW//J5p/7Hd26n9A/VUpWywwoICNKJTGxmGoW0HjkqSTp67qD3HTumNjo+oemhphQaV1NBnWik5NVUrtv/hyFNDAfP1slVqHdlYrR68T2FlS+v1FzrL3d1Ny9dtyrR/1Yrh6t25gyLvvUeurpkPypgwbIBaPXifwsuVVqXQchra+3lFX7iog0eO5+GZoLCYOnWqQkND5eHhofr162vbtm1Z9n3ggQdkMpkybK1atbL26dKlS4bnmzdvnqfnYPdArnr16umjjz7S999/rx9++EETJ05UvXr1FBcXpylTpuRFjACyITU1VYcOH1btWrWsbWazWbVr1dL+Awcy3Wf/gQOqXbuWTVudOndZ+0dFRSk2NtbmmF5eXqpSubL277/Wx9vbW2XKlNHadeuVnJys9PR0/bBihXx9fVWpYkVJUpkypeXt7a2Vq1YrNTVVKSkpWrV6tcqVLavAwMDcuwgoMFLT0rT/5BnVr/rPcBKz2az6VcK15+ipbB0j+Wqq0tIt8vEqKkm6mpYuSXL/14c+s9kstyJF9Pvhk7kYPZxJamqaDh45rrtrRFjbzGaz6taopr1/5d5dI5MuX5EkeRf3yrVjonD6+uuv1b9/f40YMUI7d+5UzZo11axZsyy/VFu8eLHOnj1r3fbu3SsXFxc9+eSTNv2aN29u0++rr77K0/O45dkg69at0zPPPKPg4GCNGDEiN2ICkAMJCQmyWCzy9fO1aff19VVsTGym+8TGxsrXN5P+sbHW5yXJ188vyz4mk0lj33lbR44c0WPtnlDrR9tq8ZKlemvMaBUvXlyS5OnpqfffHav1Gzbo0cce12PtntBvO3ZozOjR1vlVuL3EXrqsdIuhEsWL2bSX8PbShfjMhzP918TFaxTgU9yaiIQGlVSwv48mLVmrhKQrSk1L08yVPyk6NiHbx8TtJy4xUekWi/z/MyzJ38dbMXHxufIaFotFH82cpxpVKim8XOZzepC/nGnF6gkTJqhHjx7q2rWrIiIi9PHHH8vT01MzZszItL+/v7+CgoKs25o1a+Tp6ZkhiXB3d7fp5/ef3925LUdJxN9//63Ro0crLCxMDz/8sEwmk5YsWaKoqKhs7Z+SkqKEhASbLdWw5CQUAPnMMAxNnTZNvr6+Gv/++/po4odq2OAejRw5Shf/NyciJSVFH078SNUiIvThhA/0wfhxCi1fXsNHjlRKCuOLkdGMlZu1avteTejVXu6urpIkVxcXffBie52Ivqj7+7+ne155W9sPHlOj6hVlNhXeccnIex9Mn6ujJ09pVP9e+R0KCqDMPtdm9bvt6tWr2rFjhyIjI61tZrNZkZGR2vK/YcI38/nnn6tDhw7y8rKtim3cuFGlSpVS5cqV1atXL128eDHnJ5UN2U4iUlNT9c0336hZs2aqXLmydu3apXHjxslsNmvo0KFq3ry5XP/3g/5mxo4dKx8fH5ttgSUmxycB4NqwIrPZrLjYOJv2uLg4+fln/m2En59fhknXcXFx1m8vrv8ZFxubZZ9du3dr27btGjx4kKpVi1ClihXV++WX5eburrVrr83d2bBxo6LPnVP/fn1V+Y47VLVKFQ0a+LqioqK05ddfb/XUUQD5FfOUi9mki4m2FYKLCUkq6VMsi72umb36Z81Y+ZP+79XndEeZIJvnIsqHaMGwXto8cbDWvD9A0159TvGXrqh0ybz9xg0Fl2/x4nIxmzNUHWLiEzJUJ3Lig+lz9cuO3Zo8arBKlfC/5eMhb+TnLV4z+1w7duzYTOO8cOGC0tPTMwzlDQwMzNaX8du2bdPevXv1/PPP27Q3b95cc+bM0bp16/Tee+/pxx9/VIsWLZSenp7zi3oT2U4iSpcurcmTJ6tdu3Y6ffq0Fi9enOO7MQ0ZMkTx8fE221Nm/mMCt8LV1VWVKlbUrt27rG0Wi0W7du1S1SpVMt2napUq2rVrt03bzt9/t/a/Xg7dtfufPkmXL+vAwYOqWvVan+vftvz3m2CTySTDMKx9rk/0us5sNl/rYzFyeMYoyFyLFFHVciHatv+Ytc1isWjbgaOqEZ71cJCZq37S9O83aVqfZ1UttHSW/YoX9ZB/cS+diL6ofSfO6IFaWd/GGLc3V9ciqlwhVL/9sc/aZrFYtGPPPlW/o0KOj2sYhj6YPlebtu3QpJEDFRIYkBvh4jaU2efaIUOG5Mlrff7557rzzjtVr149m/YOHTqoTZs2uvPOO9W2bVstX75c27dv18aNG/MkDsmOJCItLc36IeBWxzC7u7vL29vbZnM1Fd7FOuzh4uUp75pV5F3z2gc4z7Ay8q5ZRR5luW81pMcfe0wrVq7SmrVrdfLkSU2eOlXJKcl6+KGHJEnjxn+gGTNnWfu3fbSNftuxQ4sWL9bff/+tuV98qUOHDqtN60ckXUsEHmv7qL6aP19bfv1Vx44d1/jxH6hECX81bNBA0rVEpFixYhr/wQQdPXpUp06d1vTPP1d0dLR1vYm7atfWpUuXNHXaNJ08eVLHT5zQBxM+lIuLi2rUrOHYiwSHeS6ygRb/tEPfbdmlo2fP6+153+vK1VQ92vDawqRvzlysSUv+udPczJU/adp3GzSy86MKKeGrC/GJuhCfqMv/uqXm6h1/avvBYzp1PkYbdh3Qix/NUZNaVdQwoqLDzw8FR/vWzbRs7Y/6YcNPOn7qjMZ/OkfJKSlq9eB9kqQxkz7V/33xjbV/amqa/jp2Qn8dO6HUtHSdvxirv46d0Kmz0dY+H0yfq9WbftHIvi/Ks6iHLsbG6WJsnFK4nTD+I7PPte7u7pn2LVmypFxcXBQdHW3THh0draCgoEz3uS4pKUnz589X9+7dbxpTeHi4SpYsqcOHD2f/ROyU7cXmzpw5o0WLFunzzz/Xq6++qhYtWujZZ5+1+WYRec+nTnU1WDfX+jhi/BuSpL/nLNae7nmT9cJ5NG58v+IT4jV37hfXFpsLD9dbo0dbhx6dO3/eZhJYRESEBg18XbPnzNWsWbMVUrq0hg97U6GhodY+Tz7xhJKTkzVp8mRdupSkatUi9NboMXJzc5Mk+fj46K3RozVrzhwNGvKG0tPSVK58eY0YNsy6kFzZsmU1asQIfTFvnvq9NkAmk0kVK1TQW2NGq4Q/VcjbVbO7qyv2UpL+77sNupBwSZXLBGlan2dVwvvacKazMfE2v0MWbNqu1LR0Dfhkgc1xXniksXq1biJJuhCfqA++WaWLCZcU4FNcj9xTUz1b3e+4k0KBFNmovuLiE/XZ/CWKiYtXpbBy+uDN16zDmaIvXLR5r12IjVXXAf/cDOar71bqq+9Wqna1ypoy+trv0iWr1kuSeg+3vYX9Gy93tyYnKDhyMsE5P7i5ualOnTpat26d2rZtK+la5WzdunXq3bv3Dff95ptvlJKSomefffamr3Pq1CldvHhRwcF59yWzybg+3sAOR44c0cyZMzV79mydPn1aTz/9tLp06aIHH3wwx1WK710pRcMxIg58n98hoJAI+nt7foeAQiKpZGh+h4BComT1BvkdQqaOP/9ovr126Gff2tX/66+/VufOnfXJJ5+oXr16mjhxohYsWKADBw4oMDBQnTp1UunSpTPMq7jvvvtUunRpzZ8/36b90qVLGjVqlNq1a6egoCAdOXJEAwcOVGJiov74448sqyK3KtuViH+rUKGC3nrrLY0ePVorV67UjBkz9Mgjj6h48eK6cOFCbscIAAAAZMlZKhGS1L59e50/f17Dhw9XVFSUatWqpZUrV1onW588eVJms+0w/4MHD+qnn37S6kwWj3VxcdGePXs0e/ZsxcXFKSQkRA8//LDGjBmTZwmElMNKRGbOnz+vuXPnqn///jnan0oEHIVKBByFSgQchUoEHKWgViJO9Gybb69d/tOl+fba+SlHlQhJ2rFjh/bv3y9JqlatmmrXrp3jBAIAAADIKZOZG/Q4mt1JxLlz59ShQwdt3LjRutJtXFycmjRpovnz5ysggFugAQAAALczu9O2V155RYmJifrzzz8VExOjmJgY7d27VwkJCerTp09exAgAAACgALG7ErFy5UqtXbtWVatWtbZFRERo6tSpevjhh3M1OAAAAOBmnGli9e3C7kqExWKRq6trhnZXV1dZLJZcCQoAAABAwWV3EvHggw/q1Vdf1ZkzZ6xtp0+fVr9+/dS0adNcDQ4AAAC4GZPZnG9bYWX3mU+ZMkUJCQkKDQ1VhQoVVKFCBYWFhSkhIUGTJ0/OixgBAAAAFCB2z4koW7asdu7cqbVr1+rAgQOSpKpVqyoyMjLXgwMAAABQ8NidRMyZM0ft27fXQw89pIceesjafvXqVc2fP1+dOnXK1QABAACAGzIxsdrR7B7O1LVrV8XHx2doT0xMVNeuXXMlKAAAAAAFl92VCMMwZMok2zt16pR8fHxyJSgAAAAgu7jFq+NlO4moXbu2TCaTTCaTmjZtqiJF/tk1PT1dx44dU/PmzfMkSAAAAAAFR7aTiLZt20qSdu3apWbNmqlYsWLW59zc3BQaGqp27drleoAAAAAACpZsJxEjRoyQJIWGhqp9+/by8PDIs6AAAACA7CrM6zXkF7vnRHTu3Dkv4gAAAADgJOxOIsxmc6YTq69LT0+/pYAAAAAAezCx2vHsTiIWL15sk0Skpqbq999/1+zZszVq1KhcDQ4AAABAwWN3EnF9gvW/PfHEE6pWrZq+/vprde/ePTfiAgAAALKFORGOl2tX/J577tG6dety63AAAAAACqhcSSKuXLmiSZMmqXTp0rlxOAAAAAAFmN3Dmfz8/GzmRBiGocTERBUtWlRffvllrgYHAAAA3AwTqx3P7iRi4sSJNo/NZrMCAgJUv359nT59OrfiAgAAAFBA3fI6EYmJifrqq680YsQI/fbbb9ziFQAAAA5FJcLxcjwnYtOmTercubOCg4M1fvx4NWnSRL/++mtuxgYAAACgALKrEhEVFaVZs2bp888/V0JCgp566imlpKRo6dKlioiIyKsYAQAAABQg2a5EtG7dWpUrV9aePXs0ceJEnTlzRpMnT87L2AAAAICbM5vzbyuksl2JWLFihfr06aNevXqpUqVKeRkTAAAAgAIs2+nTTz/9pMTERNWpU0f169fXlClTdOHChbyMDQAAALgpk8mUb1thle0k4p577tH06dN19uxZvfDCC5o/f75CQkJksVi0Zs0aJSYm5mWcAAAAAAoIuwdyeXl5qVu3bvrpp5/0xx9/6LXXXtO7776rUqVKqU2bNnkRIwAAAJAlk9mcb1thdUtnXrlyZb3//vs6deqUvvrqq9yKCQAAAEABlivpk4uLi9q2bavvvvsuNw4HAAAAoACze8VqAAAAoCBhxWrHK7wDuQAAAADkCJUIAAAAOLdCPME5v3DFAQAAANiFJAIAAACAXRjOBAAAAKfGxGrHoxIBAAAAwC5UIgAAAODUTCa+F3c0rjgAAAAAu1CJAAAAgHNjToTDUYkAAAAAYBeSCAAAAAB2YTgTAAAAnJqJFasdjisOAAAAwC5UIgAAAODUWGzO8ahEAAAAALALSQQAAAAAuzCcCQAAAM6NFasdjisOAAAAwC5UIgAAAODUmFjteFQiAAAAANiFSgQAAACcG4vNORxXHAAAAIBdSCIAAAAA2IXhTAAAAHBqJhMTqx2NSgQAAAAAu1CJAAAAgHNjYrXDccUBAAAA2IUkAgAAAIBdGM4EAAAAp8aK1Y5HJQIAAACAXahEAAAAwLmZ+F7c0bjiAAAAAOxCJQIAAADOjTkRDkclAgAAAHCgqVOnKjQ0VB4eHqpfv762bduWZd9Zs2bJZDLZbB4eHjZ9DMPQ8OHDFRwcrKJFiyoyMlKHDh3K03MgiQAAAAAc5Ouvv1b//v01YsQI7dy5UzVr1lSzZs107ty5LPfx9vbW2bNnrduJEydsnn///fc1adIkffzxx9q6dau8vLzUrFkzJScn59l5kEQAAADAqZlM5nzb7DVhwgT16NFDXbt2VUREhD7++GN5enpqxowZNzg/k4KCgqxbYGCg9TnDMDRx4kS9+eabevTRR1WjRg3NmTNHZ86c0dKlS3NyObOFJAIAAADIoZSUFCUkJNhsKSkpmfa9evWqduzYocjISGub2WxWZGSktmzZkuVrXLp0SeXLl1fZsmX16KOP6s8//7Q+d+zYMUVFRdkc08fHR/Xr17/hMW9VgZlYHXHg+/wOAYXEviqt8jsEFBIeferkdwgoJOJPXsjvEFBIlPxmdX6HkLl8nFg9duxYjRo1yqZtxIgRGjlyZIa+Fy5cUHp6uk0lQZICAwN14MCBTI9fuXJlzZgxQzVq1FB8fLzGjx+vhg0b6s8//1SZMmUUFRVlPcZ/j3n9ubxQYJIIAAAAwNkMGTJE/fv3t2lzd3fPteM3aNBADRo0sD5u2LChqlatqk8++URjxozJtdexF0kEAAAAkEPu7u7ZThpKliwpFxcXRUdH27RHR0crKCgoW8dwdXVV7dq1dfjwYUmy7hcdHa3g4GCbY9aqVStbx8wJ5kQAAADAqZnM5nzb7OHm5qY6depo3bp11jaLxaJ169bZVBtuJD09XX/88Yc1YQgLC1NQUJDNMRMSErR169ZsHzMnqEQAAAAADtK/f3917txZdevWVb169TRx4kQlJSWpa9eukqROnTqpdOnSGjt2rCRp9OjRuueee1SxYkXFxcVp3LhxOnHihJ5//nlJ1+7c1LdvX7311luqVKmSwsLCNGzYMIWEhKht27Z5dh4kEQAAAHBuJudZsbp9+/Y6f/68hg8frqioKNWqVUsrV660Tow+efKkzP+qcMTGxqpHjx6KioqSn5+f6tSpo19++UURERHWPgMHDlRSUpJ69uypuLg43XvvvVq5cmWGRelyk8kwDCPPjm6HY0cO53cIKCS4OxMc5S7uzgQH4e5McJQqBfTuTJdnjMi31/bsNurmnW5DVCIAAADg3Oycm4BbxxUHAAAAYBeSCAAAAAB2YTgTAAAAnJsTTay+XVCJAAAAAGAXKhEAAABwavYu+oZbxxUHAAAAYBeSCAAAAAB2YTgTAAAAnJuJ78UdjSsOAAAAwC5UIgAAAODczNzi1dGoRAAAAACwC0kEAAAAALswnAkAAABOzcTEaofjigMAAACwC5UIAAAAODcmVjsclQgAAAAAdqESAQAAAOfGnAiH44oDAAAAsAtJBAAAAAC7MJwJAAAAzs3ExGpHoxIBAAAAwC5UIgAAAODczHwv7mhccQAAAAB2IYkAAAAAYBeGMwEAAMC5sU6Ew3HFAQAAANiFSgQAAACcm5lbvDoalQgAAAAAdqESAQAAAOfGnAiH44oDAAAAsAtJBAAAAAC7MJwJAAAAzs3ExGpHoxIBAAAAwC5UIgAAAODczHwv7mhccQAAAAB2IYkAAAAAYBeGMwEAAMC5MbHa4ahEAAAAALALlQgAAAA4N1asdjiuOAAAAAC7UIkAAACAc+MWrw7HFQcAAABgF5IIAAAAAHZhOBMAAACcG7d4dTi7KxGGYejkyZNKTk7Oi3gAAAAAFHA5SiIqVqyov//+Oy/iAQAAAOxjMuffVkjZfeZms1mVKlXSxYsX8yIeAAAAAAVcjtKnd999V6+//rr27t2b2/EAAAAAKOByNLG6U6dOunz5smrWrCk3NzcVLVrU5vmYmJhcCQ4AAAC4KSZWO1yOkoiJEyfmchgAAAAAnEWOkojOnTvndhwAAABAzrBitcPd8joRycnJunr1qk2bt7f3rR4WAAAAQAGVoyQiKSlJgwYN0oIFCzK9S1N6evotBwYAAABkh8GcCIfLUe1n4MCBWr9+vf7v//5P7u7u+uyzzzRq1CiFhIRozpw5uR0jAAAAgAIkR5WIZcuWac6cOXrggQfUtWtX3XfffapYsaLKly+vL7/8Uh07dsztOAEAAAAUEDmqRMTExCg8PFzStfkP12/peu+992rTpk25Fx0AAABwM6xY7XA5OvPw8HAdO3ZMklSlShUtWLBA0rUKha+vb64FBwAAAKDgydFwpq5du2r37t1q3LixBg8erNatW2vKlClKTU3VhAkTcjtGAAAAIGuFuCKQX3KURPTr18/698jISB04cEA7duxQxYoVVaNGjVwLDgAAAEDBk6Mk4u+//1bZsmWtj8uXL6/y5cvnWlAAAAAACq4c1X5CQ0PVuHFjTZ8+XbGxsbkdEwAAAJBthsmUb1thlaMk4rffflO9evU0evRoBQcHq23btlq4cKFSUlJyOz4AAAAABUyOkojatWtr3LhxOnnypFasWKGAgAD17NlTgYGB6tatW27HCAAAAGSNW7w6XI7mRFxnMpnUpEkTNWnSRL169VL37t01e/ZszZgxI7fiu218t2y5Fi5apNjYWIWHhemlXi+qcuXKWfbftHmz5sz9QtHR0SodEqJu3bqq3t13W583DENzv/hCK1auUlJSkiIiquqVl19W6dKlrX1OnTqtz2Z8rn379istNVWhYWHq/NyzqlmzprXPwb/+0syZs3To8GGZTNIdd1TW8926WtcBQeHlf29dhb/WXT53VZdHSCn91u4lRX+3Lr/DgpPxbPSQvB54RC7FfZR65qQSlsxW6t9Hsuxv8vBU8ZZPyePOu2X2LKb02AtKWDpXKQd2SZIChn6kIv4BGfZL+nm1EhbPyqOzgDPybdZaJdo8KRdff6WcOKroGVOVfPhglv39Wj4m32aPyLVkKaUnJCjx1806P+9zGampDowacB63lD6dOnVK77//vmrVqqV69eqpWLFimjp1am7Fdtv48cdNmj59up595hlNmTxJ4eFhGjpsmOLi4jLtv2/fPr373vtq9vDDmjp5kho0aKDRY97S8ePHrX2+WbhQ3363TH16v6yJH06Qh4eHhg4bpqtXr1r7jBg5Uunp6Xp37DuaPOkjhYeFafjIUdbFAa9cuaI3hw1XQECAJn44QePHjZNn0aIaOmyY0tLS8vKSwAm4eHkqYc9B7e0zKr9DgZPyqHWPvNs8q0urF+vCh0OVduak/HsOlrmYd+Y7uLjI/4UhcvELUOzsj3T+3dcUv2C60uNjrF0uTnxT0SN7WbeLH78jSUrevdURpwQnUbxhY5Xq/IIufPOFjg96SSknjqrs0Hfk4u2baX/ve5sooGN3XfzmCx3r+7zO/t8EFW/YWAHPMLrCaZhM+bcVUjlKIj755BM1btxYoaGhmjNnjtq3b68jR45o8+bNevHFF3M7Rqe3eMkSNW/eXA8//JDKlyunV3r3lru7h1atXp1p/6Xffqe6deroySfaqVy5curc6TlVrFBB3y1bLulaFWLJ0m/1dIf2atCggcLDwvT6a6/p4sUY/bJliyQpPj5ep8+cUfsnn1R4WJhKly6tbl27KCUlRcdPnJAk/f33KSUmJqrTc8+qbJkyCi1fXh2feUaxsXE6d+6cYy4OCqzzqzbprxETFf3t2vwOBU7K6/6WuvzrBl3Z/qPSok8rftHnMlJTVLRe40z7e9Z7QGbPYoqdOUGpx/9SeuwFXT16QGlnT1r7WJISZUmMt24eEbWVdiFKV4/sd9RpwQn4P9JO8etWKH7jal09dVJRn34ky9UU+TzYLNP+RStH6MrBP5Xw0walno/W5T07lPjzBnlUzHrEAHArpk6dqtDQUHl4eKh+/fratm1bln2nT5+u++67T35+fvLz81NkZGSG/l26dJHJZLLZmjdvnqfnkKMk4q233lL9+vW1Y8cO7d27V0OGDOEWr1lITU3VocOHVbtWLWub2WxW7Vq1tP/AgUz32X/ggGrXrmXTVqfOXdb+UVFRio2NtTmml5eXqlSurP37r/Xx9vZWmTJltHbdeiUnJys9PV0/rFghX19fVapYUZJUpkxpeXt7a+Wq1UpNTVVKSopWrV6tcmXLKjAwMPcuAoDCx8VFrmXClHJo7z9thqGUv/bKrXylTHdxr1ZHqScOyefxrio18v9UcsB78mr6aNbf9Lm4qGide3V52495cAJwWkWKyCO8kpL2/P5Pm2Ho8p7fVfSOqpnucuXgPnmEV7ImDa6lguRVu56Sdmb9wQ7Iqa+//lr9+/fXiBEjtHPnTtWsWVPNmjXL8gvcjRs36umnn9aGDRu0ZcsWlS1bVg8//LBOnz5t06958+Y6e/asdfvqq6/y9DzsnhORlpambt26qUePHipTpkxexHRbSUhIkMVika+fr027r6+v/v7770z3iY2Nla9vxv7Xb6d7/U9fP78s+5hMJo19522NHj1Gj7V7QiaTSb6+vnprzGgVL15ckuTp6an33x2rUWPe0lfz50uSQkJC9PaYMXJxcbml8wZQuJm9isvk4iJLYrxNu+VSvIqUCsl0nyIlSsmlYoSu7PxZMZ+9ryIlA+XzeFeZXFx0afXiDP09qteVycNTV7aTROAfRYp7y+TiorR421vQp8XHyrN02Uz3Sfhpg1yK+6j8mAmSTDIVKaLY1ct0ccl8B0SMXGF2ngnOEyZMUI8ePdS1a1dJ0scff6zvv/9eM2bM0ODBgzP0//LLL20ef/bZZ1q0aJHWrVunTp06Wdvd3d0VFBSUt8H/i91XvEiRIpowYcItjZlPSUlRQkKCzcbtYXOXYRiaOm2afH19Nf799/XRxA/VsME9GjlylC7+b05ESkqKPpz4kapFROjDCR/og/HjFFq+vIaPHMm/BwDHM5lkuZSg+G8+U9qpY0re9asurf1Wng2aZtrds34TpRzYLUtCnGPjxG3HM6KGSjzeQVHTJ+v4oJd0atwoFburvkq065jfocEJ2PO59urVq9qxY4ciIyOtbWazWZGRkdryvyHpN3P58mWlpqbK39/fpn3jxo0qVaqUKleurF69eunixYs5P6lsyFHa9uCDD+rHH3P+zc/YsWPl4+Njs/3fx5/k+HgFmbe3t8xms+Ji42za4+Li5Ofvl+k+fn5+GSZdx8XFye9/lYfrf8b9Z6G/f/fZtXu3tm3brsGDB6latQhVqlhRvV9+WW7u7lq79toY9w0bNyr63Dn179dXle+4Q1WrVNGgga8rKipKW3799VZPHUAhZklKlJGeLnNxH5t2czEfWRLjMt0nPSFOaeejJMOwtqWdOy0Xbz/pP9VRF7+ScqtUXZe3bsj12OHc0hITZKSnq4iP7e/YIj5+SouLyXSfkh06K37TOsWvX6mUk8d1advPOj9vpko81r5QT5x1Jvm52Fxmn2vHjh2baZwXLlxQenp6hmHjgYGBioqKyta5Dho0SCEhITaJSPPmzTVnzhytW7dO7733nn788Ue1aNFC6enpOb+oN5GjW7y2aNFCgwcP1h9//KE6derIy8vL5vk2bdrccP8hQ4aof//+Nm1nTmU+tMfZubq6qlLFitq1e5caNmwgSbJYLNq1a5dat34k032qVqmiXbt267G2ba1tO3//XVWrVJEkBQUFyc/PT7t271aFChUkSUmXL+vAwYNq1aqlJFkzYPN/fviZTCYZ//sFnZKSYp18c53ZbL7Wx2IIAHIsPV2pp47JvVI1pez97VqbyST3StWU9HPmN5VIPfaXPO5qeO1D2/9+TrkEBCs9Plb6zy/Conc3luVSvFL2/57ZoVCYpaUp+eghed1ZS5e2/3KtzWSS5521FLvyu0x3Mbt7SBaLTZthSbfu++/EFvivzD7Xuru758lrvfvuu5o/f742btwoDw8Pa3uHDh2sf7/zzjtVo0YNVahQQRs3blTTpplXc29VjpKIl156SdK1MV3/ZTKZbpr1uLu7Z7i4F/PoYhcEjz/2mMZPmKBKlSqp8h13aMm33yo5JVkPP/SQJGnc+A9UokQJdevaRZLU9tE2en3QYC1avFj17r5bG3/cpEOHDuvVV16RdO0aP9b2UX01f75CQkIUFBikOXPnqkQJfzVscC1RqVqliooVK6bxH0xQx2eelpubu1asWqno6GjrehN31a6tzz6foanTpqlN69ayGIYWLPhGLi4uqlGzhuMvFAoUFy9PeVUsZ33sGVZG3jWr6GpMvJL/PpuPkcFZJG36Qb4dXlTq30eVevKIPO9vIZObh678byK0z9O9ZImPUeIPX1/rv2WNPO99SN5tOylp8yoVCQhSsaaP6vLmlbYHNplU9O77deW3zRk++AGSFLN8kYJffl1XjhxS8uED8mv1uMzuHorfsEqSFNz7daXFXNT5edfWtbr026/ye+RxJR87ouTDB+QaFKKADp11acevvMdwU5l9rs1KyZIl5eLioujoaJv26Ojom85nGD9+vN59912tXbtWNWrc+HNaeHi4SpYsqcOHDxesJMLCfyi7NG58v+IT4jV37hfXFpsLD9dbo0dbhx6dO39eJvM/1YCIiAgNGvi6Zs+Zq1mzZiukdGkNH/amQkNDrX2efOIJJScna9Lkybp0KUnVqkXordFj5ObmJkny8fHRW6NHa9acORo05A2lp6WpXPnyGjFsmHUhubJly2rUiBH6Yt489XttgEwmkypWqKC3xoxWif+Ms0Ph41Onuhqsm2t9HDH+DUnS33MWa0/3IfkVFpxI8q5fleDlrWLNnpCLt69ST59QzPR3ZbmUIEly8S0hGf/8PrHExSjm0/fk/eizChjwrtLjY5W0eaWS1tt+e+xWqbqK+Afo8taNjjwdOJHEX36Ui7ePAtp3kouvn1KOH9Xfbw9VenycJMm1ZCmb6sKFRV/KMAwFPN1ZRfxLKj0hXpd++1Xnv5qZT2cAuznJytFubm6qU6eO1q1bp7b/G3FisVi0bt069e7dO8v93n//fb399ttatWqV6tate9PXOXXqlC5evKjg4ODcCj0Dk2HcWo0uOTnZppySU8eOHL7lYwDZsa9Kq/wOAYXEXX3q5HcIKCTiT17I7xBQSFT5JvPhiPktacvSfHttrwZt7er/9ddfq3Pnzvrkk09Ur149TZw4UQsWLNCBAwcUGBioTp06qXTp0tZ5Fe+9956GDx+uefPmqVGjRtbjFCtWTMWKFdOlS5c0atQotWvXTkFBQTpy5IgGDhyoxMRE/fHHH3k2tCpHaVt6errGjBmj0qVLq1ixYjp69KgkadiwYfr8889zNUAAAADgRgyTOd82e7Vv317jx4/X8OHDVatWLe3atUsrV660TrY+efKkzp79Z9jw//3f/+nq1at64oknFBwcbN3Gjx8vSXJxcdGePXvUpk0b3XHHHerevbvq1KmjzZs351kCIeVwONPbb7+t2bNn6/3331ePHj2s7dWrV9fEiRPVvXv3XAsQAAAAuJ307t07y+FLGzdutHl8/PjxGx6raNGiWrVqVS5Fln05qkTMmTNHn376qTp27GizKFnNmjV1IItVmAEAAIA8YTLl31ZI5SiJOH36tCpWrJih3WKxKDU19ZaDAgAAAFBw5SiJiIiI0ObNmzO0L1y4ULVr177loAAAAAAUXDmaEzF8+HB17txZp0+flsVi0eLFi3Xw4EHNmTNHy5cvz+0YAQAAgCzlZIIzbk2Orvijjz6qZcuWae3atfLy8tLw4cO1f/9+LVu2TA/9bwE1AAAAALenHFUiJOm+++7TmjVrcjMWAAAAwH6FeIJzfslRJSI8PFwXL17M0B4XF2ddDRkAAADA7SlHScTx48eVnp6eoT0lJUWnT5++5aAAAAAAFFx2DWf67rvvrH9ftWqVfHx8rI/T09O1bt06hYaG5lpwAAAAwE0xsdrh7Eoi2rZtK0kymUzq3LmzzXOurq4KDQ3VBx98kGvBAQAAACh47EoiLBaLJCksLEzbt29XyZIl8yQoAAAAILsMJlY7XI7uznTs2LHcjgMAAACAk8jxLV7XrVundevW6dy5c9YKxXUzZsy45cAAAAAAFEw5SiJGjRql0aNHq27dugoODpaJEhIAAADyCxOrHS5HScTHH3+sWbNm6bnnnsvteAAAAAAUcDlKIq5evaqGDRvmdiwAAACA3QwxKsbRclT7ef755zVv3rzcjgUAAACAE8hRJSI5OVmffvqp1q5dqxo1asjV1dXm+QkTJuRKcAAAAMDNGMyJcLgcJRF79uxRrVq1JEl79+7NzXgAAAAAFHA5SiI2bNiQ23EAAAAAcBJ2JRGPP/74TfuYTCYtWrQoxwEBAAAAdmE4k8PZlUT4+PjkVRwAAAAAnIRdScTMmTPzKg4AAAAgRwwWPnY4aj8AAAAA7EISAQAAAMAuObo7EwAAAFBQsE6E43HFAQAAANiFSgQAAACcGxOrHY5KBAAAAAC7UIkAAACAU2NOhONxxQEAAADYhSQCAAAAgF0YzgQAAACnZoiJ1Y5GJQIAAACAXahEAAAAwKkxsdrxuOIAAAAA7EISAQAAAMAuDGcCAACAc2PFaoejEgEAAADALlQiAAAA4NQMvhd3OK44AAAAALtQiQAAAIBTM5gT4XBUIgAAAADYhSQCAAAAgF0YzgQAAACnxorVjscVBwAAAGAXKhEAAABwaoaYWO1oVCIAAAAA2IUkAgAAAIBdGM4EAAAAp8bEasfjigMAAACwC5UIAAAAODVWrHY8KhEAAAAA7EIlAgAAAE6NW7w6HpUIAAAAAHYhiQAAAABgF4YzAQAAwKlxi1fH44oDAAAAsAuVCAAAADg1JlY7HpUIAAAAAHYhiQAAAABgF4YzAQAAwKkxsdrxuOIAAAAA7EIlAgAAAE6NidWORyUCAAAAgF2oRAAAAMCpMSfC8bjiAAAAgANNnTpVoaGh8vDwUP369bVt27Yb9v/mm29UpUoVeXh46M4779QPP/xg87xhGBo+fLiCg4NVtGhRRUZG6tChQ3l5CiQRAAAAgKN8/fXX6t+/v0aMGKGdO3eqZs2aatasmc6dO5dp/19++UVPP/20unfvrt9//11t27ZV27ZttXfvXmuf999/X5MmTdLHH3+srVu3ysvLS82aNVNycnKenYfJMAwjz45uh2NHDud3CCgk9lVpld8hoJC4q0+d/A4BhUT8yQv5HQIKiSrfrM7vEDJ19MiRfHvt8AoV7Opfv3593X333ZoyZYokyWKxqGzZsnrllVc0ePDgDP3bt2+vpKQkLV++3Np2zz33qFatWvr4449lGIZCQkL02muvacCAAZKk+Ph4BQYGatasWerQocMtnF3WqEQAAAAAOZSSkqKEhASbLSUlJdO+V69e1Y4dOxQZGWltM5vNioyM1JYtWzLdZ8uWLTb9JalZs2bW/seOHVNUVJRNHx8fH9WvXz/LY+aGAjOxOujv7fkdAgoJD74dhoPsnLQjv0NAIRHeplx+hwDkK8OUf7d4HTt2rEaNGmXTNmLECI0cOTJD3wsXLig9PV2BgYE27YGBgTpw4ECmx4+Kisq0f1RUlPX5621Z9ckLBSaJAAAAAJzNkCFD1L9/f5s2d3f3fIrGcUgiAAAAgBxyd3fPdtJQsmRJubi4KDo62qY9OjpaQUFBme4TFBR0w/7X/4yOjlZwcLBNn1q1amX3NOzGnAgAAAA4NcMw5dtmDzc3N9WpU0fr1q2ztlksFq1bt04NGjTIdJ8GDRrY9JekNWvWWPuHhYUpKCjIpk9CQoK2bt2a5TFzA5UIAAAAwEH69++vzp07q27duqpXr54mTpyopKQkde3aVZLUqVMnlS5dWmPHjpUkvfrqq2rcuLE++OADtWrVSvPnz9dvv/2mTz/9VJJkMpnUt29fvfXWW6pUqZLCwsI0bNgwhYSEqG3btnl2HiQRAAAAcGqGEw2uad++vc6fP6/hw4crKipKtWrV0sqVK60To0+ePCmz+Z/zadiwoebNm6c333xTb7zxhipVqqSlS5eqevXq1j4DBw5UUlKSevbsqbi4ON17771auXKlPDw88uw8Csw6EVc2fpXfIaCQiFu2LL9DQCHB3ZngKNydCY5SddGa/A4hU4eOnMi3165UoXy+vXZ+ohIBAAAAp2Yo/27xWlg5T+0HAAAAQIFAEgEAAADALgxnAgAAgFNjOJPjUYkAAAAAYBcqEQAAAHBqVCIcj0oEAAAAALuQRAAAAACwC8OZAAAA4NQYzuR4VCIAAAAA2IVKBAAAAJyaYVCJcDQqEQAAAADsQhIBAAAAwC4MZwIAAIBTY2K141GJAAAAAGAXKhEAAABwalQiHI9KBAAAAAC7UIkAAACAU6MS4XhUIgAAAADYhSQCAAAAgF0YzgQAAACnxorVjkclAgAAAIBdqEQAAADAqVmYWO1wVCIAAAAA2IUkAgAAAIBdGM4EAAAAp8Y6EY5HJQIAAACAXahEAAAAwKlxi1fHoxIBAAAAwC5UIgAAAODUmBPheFQiAAAAANiFJAIAAACAXRjOBAAAAKfGxGrHoxIBAAAAwC5UIgAAAODUmFjteFQiAAAAANiFJAIAAACAXRjOBAAAAKfGxGrHoxIBAAAAwC5UIgAAAODULPkdQCFEJQIAAACAXahEAAAAwKkxJ8LxqEQAAAAAsAtJBAAAAAC7MJwJAAAATo0Vqx3vlioRV69e1cGDB5WWlpZb8QAAAAAo4HKURFy+fFndu3eXp6enqlWrppMnT0qSXnnlFb377ru5GiAAAABwI4ZhyretsMpREjFkyBDt3r1bGzdulIeHh7U9MjJSX3/9da4FBwAAAKDgydGciKVLl+rrr7/WPffcI5PpnwysWrVqOnLkSK4FBwAAAKDgyVEScf78eZUqVSpDe1JSkk1SAQAAAOQ1JlY7Xo6GM9WtW1fff/+99fH1xOGzzz5TgwYNcicyAAAAAAVSjioR77zzjlq0aKF9+/YpLS1NH330kfbt26dffvlFP/74Y27HCAAAAGTJYuR3BIVPjioR9957r3bt2qW0tDTdeeedWr16tUqVKqUtW7aoTp06uR0jAAAAgAIkx4vNVahQQdOnT8/NWAAAAAC7MSfC8XKcRKSnp2vJkiXav3+/JCkiIkKPPvqoihRhEWwAAADgdpajT/x//vmn2rRpo6ioKFWuXFmS9N577ykgIEDLli1T9erVczVIAAAAAAVHjuZEPP/886pWrZpOnTqlnTt3aufOnfr7779Vo0YN9ezZM7djBAAAALLEitWOl6NKxK5du/Tbb7/Jz8/P2ubn56e3335bd999d64FBwAAAKDgyVEl4o477lB0dHSG9nPnzqlixYq3HBQAAACQXYaRf1thle0kIiEhwbqNHTtWffr00cKFC3Xq1CmdOnVKCxcuVN++ffXee+/lZbwAAAAA8lm2hzP5+vpaV6aWJMMw9NRTT1nbjP+lYq1bt1Z6enouhwkAAACgoMh2ErFhw4a8jAMAAADIEQvrRDhctpOIxo0b52UcAAAAAJxEjiZWS9LmzZv17LPPqmHDhjp9+rQkae7cufrpp59yLTgAAADgZrjFq+Pl6BavixYt0nPPPaeOHTtq586dSklJkSTFx8frnXfe0Q8//JCrQRYW8zds0+w1P+ti/CXdUSZIgzq00J1hZTLtu2jzDi3/dbcOnzknSYooF6zebZva9L+YcEkTF6/Rr/uOKPFysu6qVF6DOrRU+cASDjkfFFyejR6S1wOPyKW4j1LPnFTCktlK/ftIlv1NHp4q3vIpedx5t8yexZQee0EJS+cq5cAuSVLA0I9UxD8gw35JP69WwuJZeXQWuF3431tX4a91l89d1eURUkq/tXtJ0d+ty++w4OT8mreR/6NPqoivv1KOH1HU51OVfPhg1v1bPSa/Zq3lWrKU0hPjlbBls85/+bmM1FQHRg04jxxVIt566y19/PHHmj59ulxdXa3tjRo10s6dO3MtuMJk1fa9+mDhKr3Q6gF9NfQF3VEmUC9N+kIxCZcy7f/bX8fV/O7qmt6/s+YM6q5APx/1+miuomMTJF2b6N5v2nydPh+rD196WvPffFHBJXz14sQ5upJy1ZGnhgLGo9Y98m7zrC6tXqwLHw5V2pmT8u85WOZi3pnv4OIi/xeGyMUvQLGzP9L5d19T/ILpSo+PsXa5OPFNRY/sZd0ufvyOJCl591ZHnBKcnIuXpxL2HNTePqPyOxTcJoo3bKxSXV7QhQVf6NjrvZR84qjKDRsrF2/fTPt739tEpZ59XhcWzNXRV7vr7LQJ8m70gAI6dnNs4MgxbvHqeDlKIg4ePKj7778/Q7uPj4/i4uJuNaZCae7aLXr83rvUtlFtVQgppTc7PiIPN1ct/eX3TPuP7d5O7R+opyplgxUWFKARndrIMAxtO3BUknTy3EXtOXZKb3R8RNVDSys0qKSGPtNKyampWrH9D0eeGgoYr/tb6vKvG3Rl+49Kiz6t+EWfy0hNUdF6mc978qz3gMyexRQ7c4JSj/+l9NgLunr0gNLOnrT2sSQlypIYb908Imor7UKUrh7Z76jTghM7v2qT/hoxUdHfrs3vUHCbKNG6neLWrlD8hlW6euqkoj75SJaUFPk2bZZp/6JVqunKgT+V8NMGpZ6PVtLuHUr4aYOKVqzi4MiBf8TExKhjx47y9vaWr6+vunfvrkuXMv9y+Xr/V155RZUrV1bRokVVrlw59enTR/Hx8Tb9TCZThm3+/Pl2x5ejJCIoKEiHDx/O0P7TTz8pPDw8J4cs1FLT0rT/5BnVr/rPtTObzapfJVx7jp7K1jGSr6YqLd0iH6+ikqSraddus+vu+s+INbPZLLciRfT74ZOZHgOFgIuLXMuEKeXQ3n/aDEMpf+2VW/lKme7iXq2OUk8cks/jXVVq5P+p5ID35NX0UcmUxThQFxcVrXOvLm/7MQ9OAABuokgReVS4Q0l7/jUywjCUtGenit4RkekuVw78KY8KleRRsbIkyTUwSMXuqqdLO7c5ImIgUx07dtSff/6pNWvWaPny5dq0aZN69uyZZf8zZ87ozJkzGj9+vPbu3atZs2Zp5cqV6t69e4a+M2fO1NmzZ61b27Zt7Y4vR3MievTooVdffVUzZsyQyWTSmTNntGXLFg0YMEDDhg3LySELtdhLl5VuMVSieDGb9hLeXjoedSFbx5i4eI0CfIpbE5HQoJIK9vfRpCVrNaxjaxV1d9UXa39VdGyCLsRnncXi9mb2Ki6Ti4ssibbfSlguxatIqZBM9ylSopRcKkboys6fFfPZ+ypSMlA+j3eVycVFl1YvztDfo3pdmTw8dWU7SQQAxytS3EcmFxelx8XatKfHx8q9dNlM90n4aYNcvH0U+taHkskkU5Eiil21TBcXf+WIkJELjNvsFq/79+/XypUrtX37dtWtW1eSNHnyZLVs2VLjx49XSEjG39nVq1fXokWLrI8rVKigt99+W88++6zS0tJUpMg/H/t9fX0VFBR0SzHmKIkYPHiwLBaLmjZtqsuXL+v++++Xu7u7BgwYoFdeeeWm+6ekpFgnY19nuZoqdzfXLPbAjcxYuVmrtu/VZ691kfv/5qi4urjogxfba+Scb3V///fkYjapfpVwNapeUSrE4/eQAyaTLJcSFP/NZ5JhKO3UMbl4+8urSatMkwjP+k2UcmC3LAlxjo8VAHLAs1oNlXz8aUVNn6wrh/bLLai0Aru9pJJPdNSFhV/md3go4DL7XOvu7i53d/ccH3PLli3y9fW1JhCSFBkZKbPZrK1bt+qxxx7L1nHi4+Pl7e1tk0BI0ssvv6znn39e4eHhevHFF9W1a1ebRaWzI0fDmUwmk4YOHaqYmBjt3btXv/76q86fP68xY8Zka/+xY8fKx8fHZhs379uchHJb8CvmKRezSRcTbSsEFxOSVNKnWBZ7XTN79c+asfIn/d+rz+mOMrYZZUT5EC0Y1kubJw7WmvcHaNqrzyn+0hWVLumX6+cA52BJSpSRni5zcR+bdnMxH1kS4zLdJz0hTmnno2xmj6WdOy0Xbz/JxcWmr4tfSblVqq7LW1mcEkD+SEuMl5GeLhdf2991Lj5+SvtPdeK6gA5dFL9preLWrVDKyeNK3Pazzs2boRKPd8h66CYKFIuRf1tmn2vHjh17S+cTFRWlUqVK2bQVKVJE/v7+ioqKytYxLly4oDFjxmQYAjV69GgtWLBAa9asUbt27fTSSy9p8uTJdseY43UiJMnNzU0RERGqV6+eihW78YfdfxsyZIji4+NtttefefRWQnFqrkWKqGq5EG3bf8zaZrFYtO3AUdUIz/wWr5I0c9VPmv79Jk3r86yqhZbOsl/xoh7yL+6lE9EXte/EGT1Qq3Kuxg8nkp6u1FPH5F6p2j9tJpPcK1XT1ROHMt0l9dhfcikZaPOL1CUgWOnxsVJ6uk3fonc3luVSvFL2Z35DAADIc2lpSj7yl7zurP1Pm8kkrxq1deWvfZnuYnJ3l2H5T5neYrHuC9xIZp9rhwwZkmnfwYMHZzqx+d/bgQMHbjmmhIQEtWrVShERERo5cqTNc8OGDVOjRo1Uu3ZtDRo0SAMHDtS4cePsfo0cDWdKSkrSu+++q3Xr1uncuXOyXP+P9j9Hjx694f6ZlXiuFPKhTM9FNtCwWUsUERqi6qGl9eW6X3XlaqoebXjth+CbMxerlK+3+jwWKUmaufInTVu2QWO7t1NICV9diE+UJHm6u8nT49q1Xb3jT/kV81Swv48OnT6n9xesUJNaVdQwomL+nCQKhKRNP8i3w4tK/fuoUk8ekef9LWRy89CV/02E9nm6lyzxMUr84etr/beskee9D8m7bSclbV6lIgFBKtb0UV3evNL2wCaTit59v678tvmfX75ANrh4ecqrYjnrY8+wMvKuWUVXY+KV/PfZfIwMzuriskUKeWWgko/8pSuHDsr/kcdkdvdQ3PpVkqTgVwYqLeaCzn85Q5J06bdf5d+6nVKOHdaVQwfkFhSigA6ddem3X/l5hpuyZ+jSa6+9pi5dutywT3h4uIKCgnTu3Dmb9rS0NMXExNx0LkNiYqKaN2+u4sWLa8mSJTbLMWSmfv36GjNmjFJSUuwagpWjJOL555/Xjz/+qOeee07BwcF2j6FCRs3urq7YS0n6v+826ELCJVUuE6RpfZ5VCe9rFZ6zMfE213nBpu1KTUvXgE8W2BznhUcaq1frJpKkC/GJ+uCbVbqYcEkBPsX1yD011bNVxlvzonBJ3vWrEry8VazZE3Lx9lXq6ROKmf6uLJeurTHi4ltCMv75pWmJi1HMp+/J+9FnFTDgXaXHxypp80olrf/O5rhulaqriH+ALm/d6MjTwW3Ap051NVg31/o4YvwbkqS/5yzWnu6Zf5sH3EjiLz/qnI+vAjp0louvn1KOHdHJt95QenycJMm1ZCmbIZoXFn4pGYYCnu6iIv4llZ4Qr8TfftX5eTPy6QxgL2dZOTogIEABARkXZ/2vBg0aKC4uTjt27FCdOnUkSevXr5fFYlH9+vWz3C8hIUHNmjWTu7u7vvvuO3l4eNz0tXbt2iU/Pz+753CYDMP+ZTJ8fX31/fffq1GjRvbumqUrG7kDAhwjbtmy/A4BhcTOSTvyOwQUEuFtyt28E5ALqi5ak98hZGrF7/m3sniL2nkzmqZFixaKjo7Wxx9/rNTUVHXt2lV169bVvHnzJEmnT59W06ZNNWfOHNWrV08JCQl6+OGHdfnyZS1ZskReXl7WYwUEBMjFxUXLli1TdHS07rnnHnl4eGjNmjUaMGCABgwYoFGj7FvwM0eVCD8/P/n7++dkVwAAACBX3Y4rR3/55Zfq3bu3mjZtKrPZrHbt2mnSpEnW51NTU3Xw4EFdvnxZkrRz505t3bpVklSxou3Q9WPHjik0NFSurq6aOnWq+vXrJ8MwVLFiRU2YMEE9evSwO74cVSK++OILffvtt5o9e7Y8PT3tftHMUImAo1CJgKNQiYCjUImAoxTUSsQPO/OvEtHyrsI5rzdHlYgPPvhAR44cUWBgoDWr+bedO3dmsScAAACQuyy32WJzziBHSUROlsYGAAAAcHvIURIxYsSI3I4DAAAAgJPI8WJzcXFx+uyzzzRkyBDFxMRIujaM6fTp07kWHAAAAHAzhpF/W2GVo0rEnj17FBkZKR8fHx0/flw9evSQv7+/Fi9erJMnT2rOnDm5HScAAACAAiJHlYj+/furS5cuOnTokM0iFi1bttSmTZtyLTgAAADgZgzDlG9bYZWjJGL79u164YUXMrSXLl1aUVFRtxwUAAAAgIIrR0mEu7u7EhISMrT/9ddf2VrKGwAAAIDzylES0aZNG40ePVqpqdcW9jCZTDp58qQGDRqkdu3a5WqAAAAAwI1YjPzbCqscJREffPCBLl26pFKlSunKlStq3LixKlasqGLFiuntt9/O7RgBAAAAFCA5ujuTj4+P1qxZo59//lm7d+/WpUuXdNdddykyMjK34wMAAABuqDDfajW/2FWJuHLlipYvX259vHz5ch0+fFhRUVH64YcfNHDgQCUnJ+d6kAAAAAAKDrsqEbNnz9b333+vRx55RJI0ZcoUVatWTUWLFpUkHThwQMHBwerXr1/uRwoAAACgQLCrEvHll1+qZ8+eNm3z5s3Thg0btGHDBo0bN04LFizI1QABAACAGzFkyretsLIriTh8+LDuvPNO62MPDw+Zzf8col69etq3b1/uRQcAAACgwLFrOFNcXJxSUlKsj8+fP2/zvMVisXkeAAAAyGuF+Var+cWuSkSZMmW0d+/eLJ/fs2ePypQpc8tBAQAAACi47EoiWrZsqeHDh2d6B6YrV65o1KhRatWqVa4FBwAAANyMYeTfVljZNZzpjTfe0IIFC1S5cmX17t1bd9xxhyTp4MGDmjJlitLS0vTGG2/kSaAAAAAACga7kojAwED98ssv6tWrlwYPHizjf+mXyWTSQw89pGnTpikwMDBPAgUAAABQMNi9YnVYWJhWrlypmJgYHT58WJJUsWJF+fv753pwAAAAwM0U5mFF+cXuJOI6f39/1atXLzdjAQAAAOAEcpxEAAAAAAWBxSi8i77lF7vuzgQAAAAAJBEAAAAA7MJwJgAAADg1JlY7HpUIAAAAAHahEgEAAACnRiXC8ahEAAAAALALlQgAAAA4NQuVCIejEgEAAADALiQRAAAAAOzCcCYAAAA4NYMVqx2OSgQAAAAAu1CJAAAAgFPjFq+ORyUCAAAAgF1IIgAAAADYheFMAAAAcGqsE+F4VCIAAAAA2IVKBAAAAJwaE6sdj0oEAAAAALtQiQAAAIBToxLheFQiAAAAANiFJAIAAACAXRjOBAAAAKfGLV4dj0oEAAAAALtQiQAAAIBTY2K141GJAAAAAGAXkggAAAAAdmE4EwAAAJyaxZLfERQ+VCIAAAAA2IVKBAAAAJwaE6sdj0oEAAAAALtQiQAAAIBToxLheFQiAAAAANiFJAIAAACAXRjOBAAAAKdmYTiTw1GJAAAAAGAXKhEAAABwaka+zqw25eNr5x8qEQAAAADsQhIBAAAAwC4MZwIAAIBTY50Ix6MSAQAAAMAuVCIAAADg1CyW/I6g8KESAQAAAMAuVCIAAADg1JgT4XhUIgAAAIACJiYmRh07dpS3t7d8fX3VvXt3Xbp06Yb7PPDAAzKZTDbbiy++aNPn5MmTatWqlTw9PVWqVCm9/vrrSktLszs+KhEAAABAAdOxY0edPXtWa9asUWpqqrp27aqePXtq3rx5N9yvR48eGj16tPWxp6en9e/p6elq1aqVgoKC9Msvv+js2bPq1KmTXF1d9c4779gVH0kEAAAAnJrlNhvOtH//fq1cuVLbt29X3bp1JUmTJ09Wy5YtNX78eIWEhGS5r6enp4KCgjJ9bvXq1dq3b5/Wrl2rwMBA1apVS2PGjNGgQYM0cuRIubm5ZTtGhjMBAAAAOZSSkqKEhASbLSUl5ZaOuWXLFvn6+loTCEmKjIyU2WzW1q1bb7jvl19+qZIlS6p69eoaMmSILl++bHPcO++8U4GBgda2Zs2aKSEhQX/++addMRaYSkRSydD8DgGFRPzJC/kdAgqJ8Dbl8jsEFBJHvzuZ3yGgkKia3wFkIT8nVo8dO1ajRo2yaRsxYoRGjhyZ42NGRUWpVKlSNm1FihSRv7+/oqKistzvmWeeUfny5RUSEqI9e/Zo0KBBOnjwoBYvXmw97r8TCEnWxzc6bmYKTBIBAAAAOJshQ4aof//+Nm3u7u6Z9h08eLDee++9Gx5v//79OY6lZ8+e1r/feeedCg4OVtOmTXXkyBFVqFAhx8fNDEkEAAAAkEPu7u5ZJg3/9dprr6lLly437BMeHq6goCCdO3fOpj0tLU0xMTFZznfITP369SVJhw8fVoUKFRQUFKRt27bZ9ImOjpYku44rkUQAAADAyRn5OrPalO2eAQEBCggIuGm/Bg0aKC4uTjt27FCdOnUkSevXr5fFYrEmBtmxa9cuSVJwcLD1uG+//bbOnTtnHS61Zs0aeXt7KyIiItvHlZhYDQAAABQoVatWVfPmzdWjRw9t27ZNP//8s3r37q0OHTpY78x0+vRpValSxVpZOHLkiMaMGaMdO3bo+PHj+u6779SpUyfdf//9qlGjhiTp4YcfVkREhJ577jnt3r1bq1at0ptvvqmXX34529WU66hEAAAAwKndbrd4la7dZal3795q2rSpzGaz2rVrp0mTJlmfT01N1cGDB613X3Jzc9PatWs1ceJEJSUlqWzZsmrXrp3efPNN6z4uLi5avny5evXqpQYNGsjLy0udO3e2WVciu0giAAAAgALG39//hgvLhYaGyvjXbanKli2rH3/88abHLV++vH744Ydbjo8kAgAAAE4tP2/xWlgxJwIAAACAXUgiAAAAANiF4UwAAABwapbbcWZ1AUclAgAAAIBdqEQAAADAqTGx2vGoRAAAAACwC0kEAAAAALswnAkAAABOjeFMjkclAgAAAIBdqEQAAADAqVkoRTgclQgAAAAAdiGJAAAAAGAXhjMBAADAqRmW/I6g8KESAQAAAMAuVCIAAADg1AwmVjsclQgAAAAAdqESAQAAAKdmYU6Ew1GJAAAAAGAXkggAAAAAdmE4EwAAAJwaE6sdj0oEAAAAALtQiQAAAIBTs1CIcDgqEQAAAADsQhIBAAAAwC4MZwIAAIBTMxjP5HBUIgAAAADYhUoEAAAAnBp3eHU8KhEAAAAA7EIlAgAAAE7NwpwIh6MSAQAAAMAuJBEAAAAA7MJwJgAAADg1g5nVDkclAgAAAIBdqEQAAADAqRmW/I6g8KESAQAAAMAuJBEAAAAA7MJwJgAAADg1CxOrHY5KBAAAAAC7UIkAAACAU+MWr45HJQIAAACAXahEAAAAwKlZLFQiHI1KBAAAAAC7kEQAAAAAsAvDmQAAAODUmFfteLeURFy9elXnzp2TxWK71ni5cuVuKSgAAAAABVeOkohDhw6pW7du+uWXX2zaDcOQyWRSenp6rgQHAAAA3IzBxGqHy1ES0aVLFxUpUkTLly9XcHCwTCZTbscFAAAAoIDKURKxa9cu7dixQ1WqVMnteAAAAAAUcDlKIiIiInThwoXcjgUAAACwm4WZ1Q6Xo1u8vvfeexo4cKA2btyoixcvKiEhwWYDAAAAcPvKUSUiMjJSktS0aVObdiZWAwAAwNGYWO14OUoiNmzYkNtxAAAAAHASOUoiGjdunNtxAAAAADlCJcLxcjQnQpI2b96sZ599Vg0bNtTp06clSXPnztVPP/2Ua8EBAAAAKHhylEQsWrRIzZo1U9GiRbVz506lpKRIkuLj4/XOO+/kaoAAAAAACpYcJRFvvfWWPv74Y02fPl2urq7W9kaNGmnnzp25FhwAAABwMxYj/7bCKkdJxMGDB3X//fdnaPfx8VFcXNytxgQAAACgAMvRxOqgoCAdPnxYoaGhNu0//fSTwsPDcyMuAAAAIFuYWO14OapE9OjRQ6+++qq2bt0qk8mkM2fO6Msvv9SAAQPUq1ev3I4RAAAAQAGSo0rE4MGDZbFY1LRpU12+fFn333+/3N3dNWDAAL3yyiu5HSMAAACAAiRHSYTJZNLQoUP1+uuv6/Dhw7p06ZIiIiJUrFix3I4PAAAAuCHDYDiTo+UoibjOzc1NERERuRULAAAAACdgVxJx9uxZTZkyRW+//bYk6d5779Xly5etz7u4uGjp0qUqXbp07kYJAAAAZMHCxGqHsyuJmDZtmmJjY62Pd+/erW7dusnf31+StGLFCn344YcaP3587kZZSCxasVbzvl2hmLh4VQwtp37dn1VEpczvdnX05Gl9Nn+xDh49rqjzF9Wn69Nq/0gzmz5zFi/Xj7/u0InTZ+Xu5qo7K1dUr+eeUvnSwY44HTgR32atVaLNk3Lx9VfKiaOKnjFVyYcPZtnfr+Vj8m32iFxLllJ6QoISf92s8/M+l5Ga6sCo4Yz8mreR/6NPqoivv1KOH1HU5zd5r7V6TH7NWl97ryXGK2HLZp3/kvcacsb/3roKf627fO6qLo+QUvqt3UuK/m5dfocFOCW77s60fPlyPf300zZtr776qkaMGKERI0Zo1KhRWrFiRa4GWFis/XmrJs+ar25PtdWMcaNUsXxZ9R8zXrHxCZn2T7maopDAAPV69kmV8PXJtM+uPw/o8eYP6tOxwzRxxOtKS09Xv9HjdSU5JS9PBU6meMPGKtX5BV345gsdH/SSUk4cVdmh78jF2zfT/t73NlFAx+66+M0XOtb3eZ39vwkq3rCxAp7p5tjA4XSKN2ysUl1e0IUFX+jY672UfOKoyg0be8P3Wqlnn9eFBXN19NXuOjttgrwbPaCAjrzXkDMuXp5K2HNQe/uMyu9QkMsMw8i3rbCyK4k4fvy4wsLCrI8feugheXl5WR9XrlxZx44dy73oCpGvl61S68jGavXgfQorW1qvv9BZ7u5uWr5uU6b9q1YMV+/OHRR57z1ydc28oDRh2AC1evA+hZcrrUqh5TS09/OKvnBRB48cz8MzgbPxf6Sd4tetUPzG1bp66qSiPv1Ilqsp8nmwWab9i1aO0JWDfyrhpw1KPR+ty3t2KPHnDfKoWNnBkcPZlGjdTnFrVyh+w6pr77VPPpIlJUW+TbN4r1WppisH/nmvJe3eoYSfNqhoxSoOjhy3i/OrNumvERMV/e3a/A4FuKmYmBh17NhR3t7e8vX1Vffu3XXp0qUs+x8/flwmkynT7ZtvvrH2y+z5+fPn2x2fXUlEamqqzp8/b328ePFiBQYGWh/HxsbKbM7R0hOFWmpqmg4eOa67a/wzSd1sNqtujWra+9eRXHudpMtXJEnexb1u0hOFRpEi8givpKQ9v//TZhi6vOd3Fb2jaqa7XDm4Tx7hlaxJg2upIHnVrqekndscETGcVZEi8qhwh5L27PynzTCUtGenit6R+Q06rhz4Ux4V/vVeCwxSsbvq6RLvNQCFQMeOHfXnn39qzZo1Wr58uTZt2qSePXtm2b9s2bI6e/aszTZq1CgVK1ZMLVq0sOk7c+ZMm35t27a1Oz675kRUrlxZv/zyi2rXrp3p85s3b9Ydd9xhdxCFXVxiotItFvn/Z1iSv4+3Tp4+myuvYbFY9NHMeapRpZLCy5XJlWPC+RUp7i2Ti4vS4mNt2tPiY+VZumym+yT8tEEuxX1UfswESSaZihRR7OplurjE/m8xUHgUKe4jk4uL0uNs32vp8bFyv9F7zdtHoW99KJn+915btUwXF3/liJABOJHbbcXq/fv3a+XKldq+fbvq1q0rSZo8ebJatmyp8ePHKyQkJMM+Li4uCgoKsmlbsmSJnnrqqQzLMPj6+mboay+7ygYdOnTQ8OHDtWfPngzP7d69W6NHj84wZyIzKSkpSkhIsNlSrl61JxTY6YPpc3X05CmN6s+K4rg1nhE1VOLxDoqaPlnHB72kU+NGqdhd9VWiXcf8Dg23Gc9qNVTy8acVNX2yjr3eS6feG6lid9VXySd4rwEoODL9XJtya/NPt2zZIl9fX2sCIUmRkZEym83aunVrto6xY8cO7dq1S927d8/w3Msvv6ySJUuqXr16mjFjRo7mdtiVRPTt21fVq1dXnTp11LJlS/Xr10/9+vVTy5YtVbduXUVERKhv3743Pc7YsWPl4+Njs3302Ry7g79d+BYvLhezWTFx8TbtMfEJGaoTOfHB9Ln6ZcduTR41WKVK+N/y8XD7SEtMkJGeriI+fjbtRXz8lBYXk+k+JTt0VvymdYpfv1IpJ4/r0rafdX7eTJV4rL1kMjkibDihtMR4GenpcvG1fa+5+Pgp7T/ViesCOnRR/Ka1ilu3Qiknjytx2886N2+GSjzegfcaABuGxci3LbPPtWPHjr2l84mKilKpUqVs2ooUKSJ/f39FRUVl6xiff/65qlatqoYNG9q0jx49WgsWLNCaNWvUrl07vfTSS5o8ebLdMdqVRLi6umrNmjUaM2aMzpw5o08++USffPKJTp8+rTFjxmjNmjVydXW96XGGDBmi+Ph4m+3V5zvZHfztwtW1iCpXCNVvf+yztlksFu3Ys0/V76iQ4+MahqEPps/Vpm07NGnkQIUEBuRGuLidpKUp+eghed1Z6582k0med9bSlb/2Z7qL2d1Dslhs2gxLunVfIFNpaUo+8pe87vzXcFiTSV41auvKX/sy3cXk7p5xiML19x7vNQAFRGafa4cMGZJp38GDB2c5+fn6duDAgVuO6cqVK5o3b16mVYhhw4apUaNGql27tgYNGqSBAwdq3Lhxdr+G3StWu7m5afDgwRo8eLDdL3adu7u73N3dbdquurnl+Hi3g/atm+ntydNVpUKYIiqFa8Hy1UpOSVGrB++TJI2Z9KlK+vup17NPSro2GfvYqdPX/p6WrvMXY/XXsRPy9PBQmeBrk90/mD5XazZv0buDX5VnUQ9djI2TJBXz9JS7e+G+3vhHzPJFCn75dV05ckjJhw/Ir9XjMrt7KH7DKklScO/XlRZzUefnzZAkXfrtV/k98riSjx1R8uEDcg0KUUCHzrq049cMyQXwbxeXLVLIKwOVfOQvXTl0UP6PPCazu4fi1v/vvfbKQKXFXND5L/95r/m3bqeUY4d15dABuV1/r/3Gew054+LlKa+K5ayPPcPKyLtmFV2NiVfy37kzBxGFT2afa7Py2muvqUuXLjfsEx4erqCgIJ07d86mPS0tTTExMdmay7Bw4UJdvnxZnTrd/Ev6+vXra8yYMUpJScn2eUg5SCL+7erVqzp37pws//lhXq5cuSz2QFYiG9VXXHyiPpu/RDFx8aoUVk4fvPmadThT9IWLMv3rm7cLsbHqOmCE9fFX363UV9+tVO1qlTVl9LXsd8mq9ZKk3sPftXmtN17ubk1OgMRffpSLt48C2neSi6+fUo4f1d9vD1V6fJwkybVkKelfYyUvLPpShmEo4OnOKuJfUukJ8br02686/9XMfDoDOIvEX37UOR9fBXTofO29duyITr71RtbvtYVfSoahgKe7WN9rib/9ak1oAXv51KmuBuvmWh9HjH9DkvT3nMXa0z3zb47hHCxOsl5DQECAAgJuPjKkQYMGiouL044dO1SnTh1J0vr162WxWFS/fv2b7v/555+rTZs22XqtXbt2yc/Pz64EQpJMRg5mUvz111/q3r27fvnlF5t2wzBkMpmUnp5u7yF1Ye8Wu/cBcuLCqBE37wTkgtvtbiEouI5+dzK/Q0Ah0So16xXm81OXkdH59tqzRgbevFMOtGjRQtHR0fr444+Vmpqqrl27qm7dupo3b54k6fTp02ratKnmzJmjevXqWfc7fPiw7rjjDv3www9q3ry5zTGXLVum6Oho3XPPPfLw8NCaNWs0YMAADRgwQKNG2bcIY44qEV27dlWRIkW0fPlyBQcH23xDDgAAADjS7filzZdffqnevXuradOmMpvNateunSZNmmR9PjU1VQcPHtTly5dt9psxY4bKlCmjhx9+OMMxXV1dNXXqVPXr10+GYahixYqaMGGCevToYXd8OapEeHl5aceOHapSJfdWDaUSAUehEgFHuR1/qaFgohIBRymolYjOw7N3x6K8MHv0ra234KxyVImIiIjQhQsXcjsWAAAAwG45WecAt8auW7xe995772ngwIHauHGjLl68mGGBDQAAAAC3rxxVIiIjIyVJTZs2tWm/lYnVAAAAAJxDjpKIDRs25HYcAAAAQI5YmIPmcDlKIho3bpzbcQAAAABwEtlOIvbs2aPq1avLbDZrz549N+xbo0aNWw4MAAAAyA7uhud42U4iatWqpaioKJUqVUq1atWSyWTKdCY8cyIAAACA21u2k4hjx45Zl84+duxYngUEAAAAoGDLdhJRvnz5TP8OAAAA5CfWiXC8bCcR3333XbYP2qZNmxwFAwAAAKDgy3YS0bZt22z1Y04EAAAAHMmwWPI7hEIn20mEhX8cAAAAAJLM9nRev369IiIilJCQkOG5+Ph4VatWTZs3b8614AAAAAAUPHYlERMnTlSPHj3k7e2d4TkfHx+98MILmjBhQq4FBwAAANyMxWLk21ZY2ZVE7N69W82bN8/y+Ycfflg7duy45aAAAAAAFFzZnhMhSdHR0XJ1dc36YEWK6Pz587ccFAAAAJBd3OLV8eyqRJQuXVp79+7N8vk9e/YoODj4loMCAAAAUHDZlUS0bNlSw4YNU3Jycobnrly5ohEjRuiRRx7JteAAAACAmzEsRr5thZVdw5nefPNNLV68WHfccYd69+6typUrS5IOHDigqVOnKj09XUOHDs2TQAEAAAAUDHYlEYGBgfrll1/Uq1cvDRkyxDr+zGQyqVmzZpo6daoCAwPzJFAAAAAABYNdSYQklS9fXj/88INiY2N1+PBhGYahSpUqyc/PLy/iAwAAAG6oMA8ryi92JxHX+fn56e67787NWAAAAAA4gRwnEQAAAEBBYDEs+R1CoWPX3ZkAAAAAgCQCAAAAgF0YzgQAAACnxsRqx6MSAQAAAMAuVCIAAADg1KhEOB6VCAAAAAB2oRIBAAAAp2YYVCIcjUoEAAAAALuQRAAAAACwC8OZAAAA4NQsFlasdjQqEQAAAADsQiUCAAAATo1bvDoelQgAAAAAdiGJAAAAAGAXhjMBAADAqRkGE6sdjUoEAAAAALtQiQAAAIBTY2K141GJAAAAAGAXKhEAAABwalQiHI9KBAAAAAC7kEQAAAAAsAvDmQAAAODULNzi1eGoRAAAAACwC5UIAAAAODUmVjselQgAAAAAdiGJAAAAAGAXhjMBAADAqRkWJlY7GpUIAAAAAHahEgEAAACnxsRqx6MSAQAAAMAuVCIAAADg1AwWm3M4KhEAAAAA7EISAQAAAMAuDGcCAACAU7MwsdrhqEQAAAAAsAuVCAAAADg1FptzPCoRAAAAAOxCEgEAAADALgxnAgAAgFNjxWrHoxIBAAAAwC5UIgAAAODUWLHa8ahEAAAAALALlQgAAAA4NeZEOB6VCAAAAKCAefvtt9WwYUN5enrK19c3W/sYhqHhw4crODhYRYsWVWRkpA4dOmTTJyYmRh07dpS3t7d8fX3VvXt3Xbp0ye74SCIAAACAAubq1at68skn1atXr2zv8/7772vSpEn6+OOPtXXrVnl5ealZs2ZKTk629unYsaP+/PNPrVmzRsuXL9emTZvUs2dPu+NjOBMAAACc2u24YvWoUaMkSbNmzcpWf8MwNHHiRL355pt69NFHJUlz5sxRYGCgli5dqg4dOmj//v1auXKltm/frrp160qSJk+erJYtW2r8+PEKCQnJdnxUIgAAAIAcSklJUUJCgs2WkpLi8DiOHTumqKgoRUZGWtt8fHxUv359bdmyRZK0ZcsW+fr6WhMISYqMjJTZbP7/9u48JsrjjQP49+VaYLnkkFtRUUEUUVQE8acGCWpBUGtQ8YqojRU8guLVyko9mlqq9UBrQgFNbY21eBERRfGgKlbZLR5AtHhEQSqeoCLH8/vD8NYXqO6igNjnk2yyOzPvvPO++2TenX13ZnHu3DmN9vfB3Imw7O7d0k1oVSoqKrBmzRosWbIEMpmspZvTqljuTm/pJrQqHGusuXCsNZ5rSzegleFY+/icPjCoxfatUCjEuwa1YmJioFAomrUdxcXFAABra2tJurW1tZhXXFyMtm3bSvJ1dHRgbm4ullEX34lopSoqKrBixYoWGemy/xaONdZcONZYc+FYY+/TkiVL8PjxY8ljyZIlDZZdvHgxBEF44yMvL6+Zj6BxPpg7EYwxxhhjjLU2MplM7TtaUVFRmDp16hvLdOzYsVHtsLGxAQDcu3cPtra2Yvq9e/fg4eEhlikpKZFsV1VVhQcPHojbq4sHEYwxxhhjjDUDKysrWFlZNUndHTp0gI2NDTIyMsRBw5MnT3Du3DlxhSdvb288evQIFy5cgKenJwDg2LFjqKmpgZeXl0b7458zMcYYY4wx9oG5desWlEolbt26herqaiiVSiiVSsl/Ori4uCAlJQUAIAgC5s2bh5UrV2L//v3Izc3F5MmTYWdnh5CQEACAq6srhg0bhhkzZiA7OxtZWVmIiIjAuHHjNFqZCeA7Ea2WTCZDTEwMTwhjTY5jjTUXjjXWXDjWWGuwfPlyJCcni6979eoFADh+/DgGDx4MAMjPz8fjx4/FMtHR0SgvL8fMmTPx6NEj+Pr6Ii0tDfr6+mKZn376CREREfDz84OWlhbGjBmDDRs2aNw+gYj4f8IZY4wxxhhjauOfMzHGGGOMMcY0woMIxhhjjDHGmEZ4EMEYY4wxxhjTCA8iGGOMtTqZmZkQBAGPHj1q6aawFiIIAvbu3QsAuHHjBgRBgFKpbNE2MfZfwoOIRjhz5gy0tbXxySefaLytQqEQ1+5tjOfPn8Pc3ByWlpb/+k+be/bsweDBg2FqagojIyO4u7sjNjYWDx48AAAkJSVBEAS4urrW23b37t0QBAFOTk6S9JcvX2Lt2rXo3bs35HI5TE1N0bNnT3zxxRe4e/duo4+HvZupU6eKy7ap4/WLLmONUVxcjLlz58LZ2Rn6+vqwtrbGgAEDsGXLFjx79qylm8c+IsXFxYiMjETHjh0hk8ng6OiIoKAgZGRk1Cvr6OiIoqIidO/eXaN98LWNscbjQUQjJCQkIDIyEidPnmz2TmbPnj1wc3ODi4tLgx8Gly1bhtDQUPTt2xeHDh3CpUuXEBcXB5VKhR07dojl5HI5SkpKcObMGcn2CQkJaNeunSStoqIC/v7+WL16NaZOnYqTJ08iNzcXGzZswP3797Fx48YmOVb24aqsrGySequrq1FTU9MkdbN399dff6FXr15IT0/H6tWrkZOTgzNnziA6OhoHDx7E0aNHW7qJ7CNx48YNeHp64tixY1i7di1yc3ORlpaGIUOGYPbs2fXKa2trw8bGBjo66q9cz9c2xt4RMY08ffqUjIyMKC8vj0JDQ2nVqlViXmJiIpmamkrKp6SkUO1pTkxMJACSR2JiIhER3bx5k0aOHElyuZyMjY1p7NixVFxcXG//gwcPpq1bt9KWLVvI399fknfu3DkCQOvXr2+w7Q8fPpS0MyIigqZPny7m3759m2QyGS1evJjat28vpq9Zs4a0tLTo4sWLDdZbU1PTYDprelOmTKHg4GAiIho0aBBFRkbSwoULqU2bNmRtbU0xMTFi2fbt20ti7/X3eO/evdSrVy+SyWTUoUMHUigUVFlZKeYDoPj4eAoKCiJDQ0P68ssvyd7enuLj4yXtuXjxIgmCQDdu3CAiori4OOrevTsZGhqSg4MDzZo1i54+fSqWr43Fffv2kaurK2lra1NhYeF7P0/s/QgICCAHBwcqKytrML+2L3j48CGFh4eTpaUlGRsb05AhQ0ipVIrlYmJiqGfPnrR9+3Zq3749mZiYUGhoKD158kQsU11dTatXryYnJyfS19cnd3d32r17t5h//PhxAkAHDx6kHj16kEwmIy8vL8rNzZW06dSpU+Tr60v6+vrk4OBAkZGR/9p+9uEYPnw42dvbN/he1V7LAFBKSgoRERUWFhIAysnJIaJ/4uPo0aPk6elJBgYG5O3tTXl5eWI9mlzb1I3HN+2PsY8NDyI0lJCQQH369CEiogMHDlCnTp3EjuZtg4hnz55RVFQUubm5UVFRERUVFdGzZ8+ourqaPDw8yNfXl/744w86e/YseXp60qBBgyR1Xbt2jWQyGT148IBKS0tJX19f/LBGRDRnzhwyMjKily9fvvEYatt58eJFMjExofLyciIi+uqrryg4OJjWrVsn+YDp7u5OAQEBjTldrInVHUSYmJiQQqGggoICSk5OJkEQKD09nYiISkpKxIFrUVERlZSUEBHRyZMnycTEhJKSkuj69euUnp5OTk5OpFAoxP0AoLZt29KPP/5I169fp5s3b9KCBQvI19dX0p6oqChJ2rp16+jYsWNUWFhIGRkZ1LVrV5o1a5aYn5iYSLq6uuTj40NZWVmUl5cnxiP7sNy/f58EQaA1a9a8tezQoUMpKCiIzp8/TwUFBRQVFUUWFhZUWlpKRK8GEUZGRjR69GjKzc2lkydPko2NDS1dulSsY+XKleTi4kJpaWl0/fp1SkxMJJlMRpmZmUT0z4c2V1dXSk9Ppz///JMCAwPJyclJ7AOvXbtGcrmc1q1bRwUFBZSVlUW9evWiqVOnNsEZYu9LaWkpCYJAq1evfmM5dQYRXl5elJmZSZcvX6aBAweSj4+PuL0m1zZ14/FN+2PsY8ODCA35+PiI3/RXVlaSpaUlHT9+nIjePogg+ucbuNelp6eTtrY23bp1S0y7fPkyAaDs7GwxbenSpRQSEiK+Dg4OlnzTPHz4cHJ3d3/rMbzeTg8PD0pOTqaamhrq1KkT7du3r94gQl9fn+bMmSOpIyQkhORyOcnlcvL29n7rPlnTqDuIqPuhvm/fvrRo0SLx9esX3Vp+fn71LtY7duwgW1tbyXbz5s2TlMnJySFBEOjmzZtE9OqbOnt7e9qyZcu/tnf37t1kYWEhvq69O/f6t9Tsw3T27FkCQL/99psk3cLCQuwLoqOj6dSpU2RiYkIvXryQlOvUqRP98MMPRPSqHzQ0NJTceVi4cCF5eXkREdGLFy/I0NCQfv/9d0kd4eHhNH78eCL650PbL7/8IuaXlpaSgYEB7dq1Syw/c+ZMSR2nTp0iLS0tev78+bucDtaEau+q1421utS9E1ErNTWVAIjvvbrXNk3i8U37Y+xjw3MiNJCfn4/s7GyMHz8eAKCjo4PQ0FAkJCS8U71Xr16Fo6MjHB0dxbRu3brBzMwMV69eBfDqt+LJycmYOHGiWGbixIlISkoSf0NOjfjz8WnTpiExMREnTpxAeXk5RowYodZ28fHxUCqVmDZtGk+m/IC4u7tLXtva2qKkpOSN26hUKsTGxsLIyEh8zJgxA0VFRZL3tk+fPpLtPDw84Orqip07dwIATpw4gZKSEowdO1Ysc/ToUfj5+cHe3h7GxsaYNGkSSktLJfXq6enVazdrPbKzs6FUKuHm5oaKigqoVCqUlZXBwsJCElOFhYW4fv26uJ2TkxOMjY3F16/H6rVr1/Ds2TP4+/tL6ti+fbukDgDw9vYWn5ubm6Nr165iv6lSqZCUlCSpIyAgADU1NSgsLGzK08LeQWOuZf/m9b7F1tYWAN7YJzZ0bdMkHjXdH2OtmfozkBgSEhJQVVUFOzs7MY2IIJPJsGnTJmhpadXr/N7XBNTDhw/jzp07CA0NlaRXV1cjIyMD/v7+6NKlC06fPo3Kykro6uqqVW9YWBiio6OhUCgwadKkBielde7cGfn5+ZK02s7R3Ny8kUfEmkLd910QhLdOVC4rK8OKFSswevToenn6+vric7lcXi8/LCwMO3fuxOLFi7Fz504MGzYMFhYWAF5NjAwMDMSsWbOwatUqmJub4/Tp0wgPD8fLly9haGgIADAwMIAgCBofK2tezs7OEAShXl/QsWNHAK/eR+BVPNna2iIzM7NeHWZmZuLzN8VqWVkZACA1NRX29vaScjKZTO02l5WV4bPPPsOcOXPq5dVdQIJ9ODp37gxBEJCXl/fOdb0eZ7X9TG2cqXtt0yQe37Q/xj42fCdCTVVVVdi+fTvi4uKgVCrFh0qlgp2dHX7++WdYWVnh6dOnKC8vF7eru2a1np4eqqurJWmurq64ffs2bt++LaZduXIFjx49Qrdu3QC8GsCMGzdOsm+lUolx48aJd0ImTJiAsrIyxMfHN3gMDa2nbm5ujpEjR+LEiROYNm1ag9uNHz8eR44cQU5OzlvPE/uw6erq1ou/3r17Iz8/H87OzvUeWlpv7iImTJiAS5cu4cKFC/j1118RFhYm5l24cAE1NTWIi4tD//790aVLF14ysRWzsLCAv78/Nm3aJOnj6urduzeKi4uho6NTL54sLS3V2le3bt0gk8lw69atenW8fscWAM6ePSs+f/jwIQoKCsTlq3v37o0rV640GNt6enqNOAusOZibmyMgIACbN29uMNbe13+DqHtt0yQeGfsv4TsRajp48CAePnyI8PBwmJqaSvLGjBmDhIQEHD58GIaGhli6dCnmzJmDc+fOISkpSVLWyckJhYWFUCqVcHBwgLGxMYYOHYoePXogLCwM69evR1VVFT7//HMMGjQIffr0wd9//40DBw5g//799dbAnjx5MkaNGoUHDx7Ay8sL0dHRiIqKwp07dzBq1CjY2dnh2rVr2Lp1K3x9fTF37tx6x5aUlIT4+HjxG+S65s+fj9TUVPj5+SEmJgYDBw5EmzZtUFBQgEOHDkFbW/vdTi5rNk5OTsjIyMCAAQMgk8nQpk0bLF++HIGBgWjXrh0+/fRTaGlpQaVS4dKlS1i5cuVb6/Px8UF4eDiqq6sxcuRIMc/Z2RmVlZXYuHEjgoKCkJWVha1btzb1IbImFB8fjwEDBqBPnz5QKBRwd3eHlpYWzp8/j7y8PHh6emLo0KHw9vZGSEgIvvnmG3HwmJqailGjRtX7WVxDjI2NsWDBAsyfPx81NTXw9fXF48ePkZWVBRMTE0yZMkUsGxsbCwsLC1hbW2PZsmWwtLQU/ztl0aJF6N+/PyIiIjB9+nTI5XJcuXIFR44cwaZNm5rqNLH3YPPmzRgwYAD69euH2NhYuLu7o6qqCkeOHMGWLVvEn6y9C3WvbZrEI2P/KS07JaP1CAwMpBEjRjSYVzsJTKVSUUpKCjk7O5OBgQEFBgbStm3bJBOrX7x4QWPGjCEzMzO1l3j99ttvyczMrMFVlyoqKsjMzIy+//57MW3Xrl30v//9j4yNjUkul5O7uzvFxsbWW+L139SdWF3b7q+//pp69uxJBgYGJJPJyMXFhebPny+ZEM6aV92J1XPnzpXkBwcH05QpU8TX+/fvJ2dnZ9LR0ZG8x2lpaeTj40MGBgZkYmJC/fr1o23bton5aGBCdq34+HgCQJMnT66X991335GtrS0ZGBhQQEAAbd++nQCoHYvsw3P37l2KiIigDh06kK6uLhkZGVG/fv1o7dq14spaT548ocjISLKzsyNdXV1ydHSksLAwsa9oaIGJuv1OTU0NrV+/nrp27Uq6urpkZWVFAQEBdOLECSL6ZyLrgQMHyM3NjfT09Khfv36kUqkk9WZnZ5O/vz8ZGRmJ/eHrS3OzD9fdu3dp9uzZ1L59e9LT0yN7e3saOXKkuJgJ1JhYXdvXEL1aDAKAZBlpda9t6sbj2/bH2MdEIHqPM5gYY4wxxhhjHz2eE8EYY4wxxhjTCA8iGGOMMcYYYxrhQQRjjDHGGGNMIzyIYIwxxhhjjGmEBxGMMcYYY4wxjfAggjHGGGOMMaYRHkQwxhhjjDHGNMKDCMYYY4wxxphGeBDBGGOMMcYY0wgPIhhjjDHGGGMa4UEEY4wxxhhjTCM8iGCMMcYYY4xp5P8PhAQwcJsvBAAAAABJRU5ErkJggg==", + "text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Ensure that the columns for predictions and the evaluations by ClinGen are properly named\n", + "# and contain numerical values\n", + "# Example columns: 'AutoACMG_Score', 'Intervar_Score', 'Genebe_Score', 'ClinGen_Score'\n", + "\n", + "# Calculate correlation matrix\n", + "tools = ['AutoACMG', 'Intervar', 'Genebe']\n", + "all_tools = tools + ['ClinGen']\n", + "\n", + "correlation_matrix = pd.DataFrame(index=all_tools, columns=all_tools)\n", + "\n", + "for tool1 in all_tools:\n", + " for tool2 in all_tools:\n", + " if tool1 == tool2:\n", + " correlation_matrix.loc[tool1, tool2] = 1.0\n", + " else:\n", + " score1 = df[f'{tool1}_Score'].dropna()\n", + " score2 = df[f'{tool2}_Score'].dropna()\n", + " common_idx = score1.index.intersection(score2.index)\n", + " correlation, _ = pearsonr(score1[common_idx], score2[common_idx])\n", + " correlation_matrix.loc[tool1, tool2] = correlation\n", + "\n", + "# Convert the correlation matrix to float\n", + "correlation_matrix = correlation_matrix.astype(float)\n", + "\n", + "# Display correlation matrix\n", + "print(correlation_matrix)\n", + "\n", + "# Save correlation matrix to CSV\n", + "correlation_matrix.to_csv('correlation_matrix.csv', index=True)\n", + "\n", + "# Visualize the correlation matrix\n", + "plt.figure(figsize=(10, 8))\n", + "sns.heatmap(correlation_matrix, annot=True, cmap='coolwarm', vmin=-1, vmax=1)\n", + "plt.title('Correlation Matrix of Prediction Scores')\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6ff30f7a", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.2" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}