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Variants of uncertain significance fundamentally limit the clinical utility of genetic information. The challenge they pose is epitomized by BRCA1, a tumour suppressor gene in which germline loss-of-function variants predispose women to breast and ovarian cancer. Although BRCA1 has been sequenced in millions of women, the risk associated with most newly observed variants cannot be definitively assigned. Here we use saturation genome editing to assay 96.5% of all possible single-nucleotide variants (SNVs) in 13 exons that encode functionally critical domains of BRCA1. Functional effects for nearly 4,000 SNVs are bimodally distributed and almost perfectly concordant with established assessments of pathogenicity. Over 400 non-functional missense SNVs are identified, as well as around 300 SNVs that disrupt expression. We predict that these results will be immediately useful for the clinical interpretation of BRCA1 variants, and that this approach can be extended to overcome the challenge of variants of uncertain significance in additional clinically actionable genes.
Our ability to predict the phenotypic consequences of an arbitrary genetic variant in a human genome remains poor. This problem is evidenced by the large numbers of variants of uncertain significance (VUS) identified in 'actionable' genes, that is, genes in which the definitive identification of a pathogenic variant would alter clinical management1. For example, heterozygous germline variants that disrupt BRCA1 markedly increase the risk of early-onset breast and ovarian cancer2,3 and are actionable, as more frequent screening or prophylactic surgery can lead to improved outcomes4,5. Clinical sequencing can identify specific variants as risk-conferring6. However, as of January 2018, most BRCA1 SNVs are classified as VUS7. VUS are typified by rare missense SNVs, but also include variants potentially affecting messenger RNA (mRNA) levels. Further illustrating the challenge associated with VUS, there are hundreds of BRCA1 SNVs that have received conflicting interpretations7.
There are two main approaches for resolving VUS. The first approach, data sharing, relies on the expectation that as BRCA1 is sequenced in more individuals, the recurrent observation of a variant in individuals who either have or have not developed cancer will enable its interpretation. However, given that the maj ority of potential variants in BRCA1 are extremely rare and that the phenotype is incompletely penetrant, it is unclear whether sufficient numbers of humans will ever be sequenced to accurately quantify...