BRCA1 NM_007294.4:c.5194-12G>A, ?

Variant summary: The BRCA1 c.5194-12G>A variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a polymorphism outcome for this variant. 2/5 splice prediction tools predict that this variant creates a novel 3' splicing acceptor site. This prediction was confirmed by two independent studies by sequencing cDNA from the patients carrying the variant of interest (Whiley_2011, Wong-Brown_2013). The studies showed that the altered splicing led to the inclusion of 10bp intronic sequence generating a downstream frameshift mutation (p.His1732Phefs). This variant has been reported in multiple patients with breast cancer and family history of HBOC. This variant is absent in 121410 control chromosomes. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic, including an expert panel. Taken together, this variant is classified as pathogenic.

The c.5194-12G>A intronic variant results from a G to A substitution 12 nucleotides upstream from coding exon 18 in the BRCA1 gene. This alteration has been classified as as a pathogenic mutation by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, mutation co-occurrence, and functional assay results (Easton DF et al. Am. J. Hum .Genet. 2007 Nov; 81(5):873-83; Whiley PJ et al. Hum. Mutat. 2011 Jun; 32(6):678-87). Multiple, independent RNA based assays indicate that this variant creates a cryptic splice acceptor site that leads to the insertion of 10 nucleotides and, consequently, a predicted protein frameshift (Ambry internal data; Whiley PJ et al. Hum. Mutat. 2011 Jun; 32(6):678-87; Théry JC et al. Eur. J. Hum. Genet. 2011 Oct; 19(10):1052-8; Wong-Brown MW et al. Clin. Genet. 2013 Nov; 84(5):505-6). This nucleotide position is highly conserved in available vertebrate species. Of note, this alteration is also designated as IVS19-12G>A in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

This sequence change falls in intron 18 of the BRCA1 gene. It does not directly change the encoded amino acid sequence of the BRCA1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast and/or ovarian cancer (PMID: 10923033, 17924331, 23278966, 25682074). ClinVar contains an entry for this variant (Variation ID: 55451). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 17924331). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 21394826, 21673748; internal data). For these reasons, this variant has been classified as Pathogenic.