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Exome sequencing is now mainstream in clinical practice, however, identification of pathogenic Mendelian variants remains time consuming, partly because limited accuracy of current computational prediction methods leaves much manual classification. Here we introduce CAPICE, a new machine-learning based method for prioritizing pathogenic variants, including SNVs and short InDels, that outperforms best general (CADD, GAVIN) and consequence-type-specific (REVEL, ClinPred) computational prediction methods, for both rare and ultra-rare variants. CAPICE is easily integrated into diagnostic pipelines and is available as free and open source command-line software, file of pre-computed scores, and as a web application with web service API.

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