BRCA2 c.631+4A>G

The c.631+4A>G variant is an intronic variant occurring in intron 7 of the BRCA2 gene. 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). This BRCA2 intronic variant is located outside of the native donor and acceptor 1,2 splice sites, and has a SpliceAI score of 0.71, predicting an impact on splicing (score threshold ≥0.2) (PP3 not applied because a PVS1 code is met). This variant is reported to result in aberrant mRNA splicing. RNAseq, minigene and RT-PCR demonstrated that the variant impacts splicing by exon skipping (PMIDs: 20455026, 31143303). Preliminary code strength determined by comparison of results to PVS1 decision tree and assessment of mRNA splicing data (PVS1 (RNA) met). The percent reference (full-length, FL) and aberrant transcripts produced from the variant allele using allele specific quantitative assessment with Capillary electrophoresis was determined to be full-length (0%) / exon skipping (100%). Final code strength determined by the rubric: PVS1 (RNA). 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, PVS1 (RNA)).