Inconsistent Handling of 5'Flank Mutation Type with Custom Filtered Mutations

[forus]

Currently, the handling of mutation records with the 5'Flank mutation type differs based on whether custom filtered mutations are specified. Here’s the observed behavior:

Default Filtered Mutations:
When using the default filtered mutations, the 5'Flank mutation is selected, and the protein change field is set to "Promoter" specifically for the TERT gene. This is achieved via a check against whiteListGenesForPromoterMutations (see MutationFilter.java#L150).

Custom Filtered Mutations:
When a custom mutation filter list is applied, the whiteListGenesForPromoterMutations check is skipped, resulting in different handling for 5'Flank mutations (see MutationFilter.java#L133).

This asymmetry in behavior seems unintended and could lead to inconsistent mutation handling depending on the filter setup.