Large-scale integration of functional assay data for the resolution of germline BRCA1 and BRCA2 variants of uncertain significance

Carriers of BRCA1 and BRCA2 pathogenic variants are at a significantly elevated risk for several cancers. Widespread germline genetic testing has led to a significant increase in the detection of variants of uncertain significance (VUSs) in these genes. To assess variant pathogenicity, we curated, harmonized, and integrated functional data for 3,247 BRCA1 and 6,177 BRCA2 missense variants derived from BRCA1/2 functional assays. Functional results were harmonized across studies by converting data into ordinal categorical variables. We applied ClinGen variant interpretation guidelines for each assay to assign evidence for or against pathogenicity. Final evidence criteria for each variant were obtained through the integration of results from different assays, and large case-control studies confirmed that benign and pathogenic variants categorized using the integrated functional framework are associated with low and high risk for breast cancer, respectively. Next, we integrated additional sources of data, leading to resolution of 80.1% of BRCA1 VUSs and 69.5% of BRCA2 VUSs and classification of 6,517 (2,345 in BRCA1 and 4,172 in BRCA2) missense variants.