Availability of benign missense variant "truthsets" for validation of functional assays: Current status and a systematic approach.

Abstract

Multiplex assays of variant effect (MAVEs) provide promising new sources of functional evidence, potentially empowering improved classification of germline genomic variants, particularly rare missense variants, which are commonly assigned as variants of uncertain significance (VUSs). However, paradoxically, quantification of clinically applicable evidence strengths for MAVEs requires construction of "truthsets" comprising missense variants already robustly classified as pathogenic and benign. In this study, we demonstrate how benign truthset size is the primary driver of applicable functional evidence toward pathogenicity (PS3). We demonstrate, when using existing ClinVar classifications as a source of benign missense truthset variants, that only 19.8% (23/116) of established cancer susceptibility genes had a PS3 evidence strength of "strong" attainable when simulating validation for a hypothetical new MAVE (also applying favorable assumption of perfect concordance). We describe a systematic framework for benign truthset construction in which all possible missense variants in a gene of interest are concurrently assessed for assignation of (likely) benignity via established ACMG/AMP combination rules, including population frequency, in silico evidence codes, and case-control signal. We apply this framework to eight hereditary breast and ovarian cancer genes, demonstrating that systematically generated benign missense truthsets allow maximum application of PS3 at greater (or equivalent) strength-reaching "moderate" for CHEK2 and "strong" for the other seven genes-than those derived from ClinVar ≥2∗ classifications alone. We propose, given many genes have few existing benign-classified missense variants, that the application of this systematic framework to disease genes more broadly will be important for leveraging full value from MAVEs.