ClinVar Genomic variation as it relates to human health

Variant summary: BRCA2 c.631+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: five predict the variant abolishes a 5' splicing donor site. At least one publication reported experimental evidence that this variant affects mRNA splicing, and demonstrated an out-of-frame skipping of exon 7 in mRNA extracted from patient derived lympoid cell line (Popp_2003). The variant was absent in 250814 control chromosomes (gnomAD). The variant, c.631+1G>A, has been reported in the literature in compound heterozygosity with a premature terminating variant (Y1894X) in individuals who were affected with Fanconi anemia (Wagner_2004, Popp_2003, Alter_2007). The variant was also reported in heterozygosity in multiple individuals affected with Hereditary Breast and Ovarian Cancer (e.g. Rebbeck_2018, Bhaskaran_2019). These data indicate that the variant is very likely to be associated with disease. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (n=3) or likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.

The variant disrupts a canonical splice site, and is therefore predicted to significantly disrupt the protein structure. Found in at least one symptomatic patient, and not found in general population data. Assessment of experimental evidence suggests this variant results in abnormal protein function.

This sequence change affects a donor splice site in intron 7 of the BRCA2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with breast cancer and Fanconi anemia (FA) (PMID: 15004464, 16825431, 27393621). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 9348). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

The c.631+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 6 of the BRCA2 gene. This mutation, in compound heterozygosity with a nonsense mutation, was previously described in two Fanconi Anemia patients in one family with a family history of early onset breast cancer (Alter BP et al. J. Med. Genet. 2007; 44:1-9). It has also been identified in unselected Chinese and Malaysian breast cancer cohorts (Sun J et al. Clin. Cancer Res. 2017 Oct;23(20):6113-6119; Li JY et al. Int. J. Cancer. 2019 Jan;144(2):281-289; Wen WX et al. J. Med. Genet. 2018 Feb;55(2):97-103). This alteration (designated as IVS7+1G>A) was demonstrated by RT-PCR to result in aberrant splicing and skipping of exon 7 (coding exon 6) (Popp H et al. Cytogenet. Genome Res. 2003 ;103(1-2):54-7). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. However, because this variant is identified in one or more patients with Fanconi Anemia it may be hypomorphic and thus, carriers of this variant and their families may present with reduced risks, and not with the typical clinical characteristics of a high-risk pathogenic BRCA2 alteration. As risk estimates are unknown at this time, clinical correlation is advised.

Canonical splice variant demonstrated to cause aberrant splicing, resulting in majority out-of-frame skipping of exon 7 (Popp et al., 2003; Fraile-Bethencourt et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Also known as 859+1G>A; This variant is associated with the following publications: (PMID: 25525159, 28490369, 29752822, 35864222, 15070707, 28152038, 28724667, 28993434, 29446198, 28888541, 31957001, 30702160, 20104584, 16825431, 31825140, 27393621, 15004464, 21719596, 32398771, 30883759)