Reclassification of a BRCA2 variant, c.8487G > A (p.Gln2829Gln) located at 3' end of exon 19, from uncertain significance to likely pathogenic based on splicing alteration: a case report.

A BRCA2 germline variant, NM_000059.4: c.8487G > A (p.Gln2829Gln), was identified in a Japanese female with multifocal breast cancer and a notable family history of BRCA2-related cancers. While this synonymous variant was reported as a variant of uncertain significance, we suspected its pathogenicity considering its location at the 3' end of exon 19. This variant is absent in gnomAD and extremely rare in ToMMo jMorp 61KJPN database, with an allelic frequency of 0.000008. All three in silico tools predicted a splicing defect. RT-PCR analysis using total RNA extracted from the patient's peripheral blood cells demonstrated skipping of entire exon 19, resulting in in-frame deletion. This observation was consistent with a previous report of in vitro minigene assay. The exon 19 encodes 52 amino acids within the single-stranded DNA oligonucleotide/oligosaccharide-binding domain, and thus the in-frame deletion was predicted to impair BRCA2 function. Collectively, we re-classified this variant as likely pathogenic.