Hi, I am trying to figure out which tool is most accurate in terms of pathogenicity prediction of TCGA SNVs level 3 data. TCGA offers SIFT, PolyPhen, and IMPACT scores for different kinds of mutations. SIFT, and PolyPhen cover mainly "Missense Mutation", while IMPACT categorizes every kind of mutation into MODERATE", "HIGH", "MODERATE", "MODIFIER".
I am ok with the IMPACT classification, however, I want numerical values rather than subjective classification like "MODERATE", "HIGH", "MODERATE", "MODIFIER". I explore some other tools like PROVEN, CAPICE, etc but all of them use GrCH37 rather than NCBI-built GrCh38 since later is used in the TCGA data.
So I am confused as to what tool I should use to find out the pathogenicity level of Missense Mutation, Silent, Frame Shift, INDEL etc.