BRCA2 c.681+1G>A

The c.681+1G>A variant is an intronic variant within the native donor 1,2 splice site occurring in intron 8 of the BRCA2 gene. This variant is present in gnomAD v4.1 but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 2.1 (based on Cosegregation LR=1.94; Pathology LR=1.08), within the thresholds for supporting evidence towards pathogenicity (LR >2.08 & ≤4.3) (PP4 met; Internal lab contributor). This variant occurs within the canonical splice donor site (+ 1,2) of intron 8. It is predicted to cause skipping of E8 and intron retention. A suspected functional rescue transcript of in-frame skipping of E8_E10 is observed (PMID: 32123317). RT-PCRseq demonstrated that the variant impacts splicing by skipping of exon 8 (Ambry internal data). The percent of aberrant transcripts produced was 20-30%, using a non-allele specific semi-quantitative assessment with sequence analysis. Potential rescue transcripts were also reported, including skipping E6_E8, which was reported at 10-25% and skipping E7_E8 at 4-6%. We estimate no full length transcript is produced by the variant allele. Appropriate code strength determined by comparison of results to PVS1 decision tree, PVS1_N/A (RNA). In summary, this variant meets the criteria to be classified as a Variant of uncertain significance for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PP4).