BRCA2 p.Phe2562Cys

The c.7685T>G variant in BRCA2 is a missense variant predicted to cause substitution of Phenylalanine by Cysteine at amino acid 2562 (p.(Phe2562Cys)). 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). Reported by three calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs:38417439, 39779857, 39779848) (PS3 met). This BRCA2 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.42, above the recommended threshold of 0.30 for prediction of impact on BRCA2 function via protein change. A SpliceAI score of 0.01 predicts no impact on splicing (score threshold <0.10) (PP3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.98 (based on Family History LR=0.98), 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). This variant has been detected in one individual with phenotype suggestive of BRCA2-Fanconi Anemia (FA). Only one clinical feature of FA (physical features, pathology findings or cancer diagnosis ≤5yr) and unknown chromosome breakage was seen in this individual. They were compound heterozygous for the variant and a pathogenic or likely pathogenic variant confirmed to be in trans. Total points equated to 0 (PM3 not met; internal lab contributor). In summary, this variant meets the criteria to be classified as a Likely pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PM2_Supporting, PS3, PP3).