BRCA2 p.Leu2587Phe

The c.7759C>T variant in BRCA2 is a missense variant predicted to cause substitution of leucine by phenylalanine at amino acid 2587 (p.Leu2587Phe). The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥20) or gnomAD v3.1 (non-cancer subset, read depth ≥20) is 0.00004512 in the European (non-Finnish) population which is within the ENIGMA BRCA1/2 VCEP threshold (>0.00002 to ≤ 0.0001) for BS1_Supporting (BS1_Supporting met). This BRCA2 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.15, which is below the recommended threshold of 0.18 for predicting no impact on BRCA2 via protein change. A SpliceAI score of 0.04 predicts no impact on splicing (score threshold <0.10) (BP4 met). Reported by four calibrated studies to exhibit protein function similar to benign control variants (PMIDs:38417439, 33293522, 39779857, 39779848) (BS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.0022 (based on Cosegregation LR=0.092; Pathology LR=0.675; Family History LR=0.0345), below the thresholds for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; PMID 34597585, 31853058). In summary, this variant meets the criteria to be classified as a Benign variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BS1_Supporting, BP4, BS3, BP5_Very strong).