Evidence for pathogenicity of BRCA2 c.8351G>A p.(Arg2784Gln) and the challenges in classification of pathogenic variants with reduced penetrance

Background The BRCA2 c.8351G>Ap.(Arg2784Gln) variant has long been classified as a variant of uncertain significance (VUS) due to conflicting evidence used in variant classification. This study aims to clarify its pathogenicity and associated risks for breast and ovarian cancer. Methods This study was conducted by the international Evidence-based Network for the Interpretation of Germline Mutant Alleles consortium. We collected data from 29 informative families with this variant. Co-segregation likelihood ratios (LRs) were calculated using the full-likelihood method to assess pathogenicity, and cancer risks were estimated with modified segregation analysis. Results Co-segregation analysis using a grid search across scaled penetrance levels for BRCA2 truncating variants yielded the strongest evidence in favour of pathogenicity, with LR maximised at approximately 20% of full penetrance (LR=11.026). Furthermore, estimated breast cancer risks were markedly higher for early onset breast cancer; women diagnosed at <50 years had a HR of 4.5, compared with a HR of 1.65 for women diagnosed at ≥50 years. The estimated lifetime risks were 25% for breast cancer and 6% for ovarian cancer. Evidence of pathogenicity was also supported by the presence of the variant allele in two patients with Fanconi anaemia. Conclusions Our results indicate that BRCA2 c.8351G>Ap.(Arg2784Gln) has a disease-causing effect, with reduced penetrance, similar to other pathogenic variants in moderate risk breast cancer genes such as ATM and CHEK2. We also provide risk-adapted recommendations for clinical management. Importantly, one should be aware of a reduced penetrance as the underlying reason for conflicting results among pieces of evidence used for variant classification.