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Next generation sequencing technologies both boost the discovery of variants in the human genome and exacerbate the challenges of pathogenic variant identification. In this study, we developed mvPPT (Pathogenicity Prediction Tool for missense variants), a highly sensitive and accurate missense variant classifier based on gradient boosting. MvPPT adopts high-confidence training sets with a wide spectrum of variant profiles, and extracts three categories of features, including scores fromdoi:10.1101/2022.01.05.475156 fatcat:dnhk4l6oqbg2jo5k6i3lutrlj4