New pathogenicity prediction scores for human: MutScore and M-CAP

[Luis Nassar]

We have two new pathogenicity prediction score tracks available in our Deleteriousness Predictions super track.

• MutScore (hg19/hg38) - MutScore is a pathogenicity predictor that integrates unsupervised features of single DNA variants with information derived from such clusters. The predictive model for MutScore was trained with a random forest approach on medically-relevant mutations and subsequently tested against various genomic databases for both hereditary conditions and cancer (ClinVar, HGMD, and DoCM) to achieve high performance.
• M-CAP (hg19) - M-CAP is a pathogenicity classifier for rare missense variants tuned to the high sensitivity required in the clinic. By combining previous pathogenicity scores (including SIFT, Polyphen-2 and CADD) with novel features and a powerful model, it yields an effective classifier, reducing a typical exome/genome rare (<1%) missense variant (VUS) list from 300 to 120, while never mistaking 95% of known pathogenic variants as benign.

See the track description page for more information and interpretation guidelines.