MAF specification TCGA : Variant_Classification

Question

[crichard]

Hello everyone,

I saw some post about how to handle with the mutation annotated files of the TCGA but I did not find an answer to my question in the forum or on the nhi/ nci wiki : MAF Specification.

I downloaded some MAF files from the Broad GDAC Firehose : Mutation_Packager_Calls_Level_3. I want to be limited to the mutations considered as functional or potentially functional. So first, I want to filter variants by their "Variant_Classification" field but I have some problems to find the meaning of some possibilities.

Can someone explain me what is "R", "RNA" "Read-through", "Splice_Site_SNP" and "Targeted_Region" and if there are considered as functional variants ?

Thanks a lot,

Best regards,

Corentin