BRCA1 p.Tyr1703Cys

The c.5108A>G variant in BRCA1 is a missense variant predicted to cause substitution of Tyr by Cys at amino acid 1703 (p.(Tyr1703Cys)). Reported by one calibrated study to affect protein function similar to pathogenic control variants (PMID:30209399) (PS3 met). This BRCA1 missense variant is within a key functional domain and a SpliceAI score of 0.03 predicts no impact on splicing (score threshold ≤0.1). The computational predictor BayesDel (noAF) gives a score of 0.42, above the recommended threshold of 0.28 for prediction of impact on BRCA1 function via protein change (PP3 met). This variant is absent from gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥25) and gnomAD v3.1 (non-cancer subset, read depth ≥25) (PM2_Supporting met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1.65 (based on Family History LR=1.65), which is above the ENIGMA BRCA1/2 VCEP threshold for BP5 (>0.48) and below PP4 (<2.08) (BP5 and PP4 not met; PMID: 31853058). In summary, this variant meets the criteria to be classified as a Likely pathogenic variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PS3, PP3, PM2_Supporting).