We are search of an archive which provides the majority of level 2 MAF putative(confirmed) somatic mutations as well as RNA-seq based transcription levels for the majority of cancers(leukemias). Given this, is Synapse (pancancer) currently the most comprehensive archive for collections of various level 2 and 3 data?

We did look at a MAF file from TCGA, and unlike the COSMIC data, there were no pathogenicity predictions (e.g. FATHMM), but rather only class memberships like "Silent," "Missense", "Deletion,", etc. We would therefore have to assume nonsense were pathogenic at least with regard to the SNVs?