Germline pathogenic BRCA1 variants predispose women to breast and ovarian cancer. Despite accumulation of functional evidence for variants in BRCA1, over half of reported single-nucleotide variants (SNVs) lack a definitive clinical interpretation. Furthermore, the extent to which variant effects are consistent across cell types remains largely unexplored. Here, we performed saturation genome editing (SGE) of BRCA1 in HAP1 cells to score 4,113 variants not previously assayed. Additionally, we developed a new SGE assay in human mammary epithelial cells (HMECs), allowing effects of variants to be compared across cell lines, drug treatments, and genetic backgrounds. We identify 538 variants impacting function via diverse mechanisms, including impairment of the BRCA1–PALB2 interaction and disruption of splicing, transcription, and translation. Function scores from experiments in HAP1 discriminate known pathogenic and benign variants with near-perfect accuracy. Intriguingly, however, nearly half of variants impacting function in HAP1 were found to be neutral when assayed in HMECs. We show that discordantly scored variants are hypomorphic and confer intermediate cancer risk. These results will be highly valuable for clinical interpretation of BRCA1 variants. Moreover, this work illustrates how revealing context-specific variant effects across cell types can enable more accurate resolution of disease risk.

The authors have declared no competing interest.

G.M.F. is supported by the Francis Crick Institute, which receives core funding from Cancer Research UK (CC2190), the UK Medical Research Council (CC2190), and the Wellcome Trust (CC2190), and a Cancer Research UK programme award (CG-MAVE). Access to the UK Biobank data has been funded by an internal research grant of the Cyprus Institute of Neurology and Genetics. BCAC is funded by Cancer Research UK (C1287-A16563) and the European Union Horizon 2020 Research and Innovation Programme (634935 and 633784 for BRIDGES and B-CAST, respectively). BRIDGES panel sequencing was supported by the European Unions Horizon 2020 Research and Innovation Program (634935) and the Wellcome Trust (v203477/Z/16/Z).

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This study made use of pre-existing clinical cohorts with genetic data available for re-analysis, namely the BRIDGES study of the Breast Cancer Association Consortium (BCAC) and the UK Biobank. Ethical oversight is maintained for both UK Biobank and BRIDGES data sets, which are accessible via researcher application. UK Biobank data access was approved by the UK Biobank Access Management Team (accessukbiobank.ac.uk) under application 102655. Access to BRIDGES data was approved by the BCAC Data Access Co-ordinating Committee (BCACmedschl.cam.ac.uk).

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