Article

An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers

2026-07-23

Abstract excerpt

Missense pathogenicity predictors such as AlphaMissense are increasingly used in clinical variant interpretation, yet they are trained on germline labels dominated by loss-of-function (LOF) variants. Using an openly licensed, reproducible benchmark of 768 Cancer Gene Census genes scored with 49 predictors (labels from CIViC, COSMIC, cancerhotspots, ClinVar and gnomAD), we show that 42 of 49 tools (86%) score oncog...

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Literature Corpus work: cc61bc79-c9ab-534b-af2c-86e067a554bb
DOI: 10.64898/2026.07.16.739080

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