ClinVar Genomic variation as it relates to human health

This variant causes an A to G nucleotide substitution at the +3 position of intron 2 of the BRCA2 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. RNA studies have shown that this variant resulted in the skipping of exon 2, deleting the translation start codon (PMID: 24302565, 30883759), that is expected to abolish expression of the full-length wild-type protein. This variant has been detected in an individual affected with breast cancer (PMID: 24302565). This variant also has been observed in trans with a pathogenic truncation variant in BRCA2 in an individual affected with Fanconi anemia (PMID: 28185119). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic.

The c.67+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 1 in the BRCA2 gene. This nucleotide position is highly conserved in available vertebrate species. This alteration has been reported in an Australian proband with bilateral breast cancer and a family history of breast cancer (Parsons MT et al. Mol. Carcinog. 2015 Jul;54(7):513-22). This alteration has also been reported in a compound heterozygous state (with BRCA2 c.5771_5774delTTCA) in an individual with Fanconi anemia (Feben C et al. Fam. Cancer 2017 07;16(3):441-446). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Using two different splice site prediction tools, this alteration is predicted by BDGP to abolish the native splice donor site, but is predicted to weaken (but not abolish) the efficiency of the native splice donor site by ESEfinder. Additionally, Parsons et al. performed RNA studies on patient DNA which revealed that this alteration causes skipping of coding exon 1 (also designated as exon 2); however, authors were not able to quantitatively assess the extent of aberrant RNA transcript in this patient (Parsons MT et al. Mol. Carcinog. 2015 Jul;54(7):513-22). Based on the majority of available evidence to date, this variant is likely to be pathogenic. 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.

This sequence change falls in intron 2 of the BRCA2 gene. It does not directly change the encoded amino acid sequence of the BRCA2 protein. RNA analysis indicates that this variant induces altered splicing and is likely to result in the loss of the initiator methionine. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast cancer and Fanconi anemia (PMID: 24302565, 28185119). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 826563). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 2, and is expected to result in the loss of the initiator methionine (PMID: 24302565, 30883759). Other variant(s) that result in the disruption of the initiator methionine have been determined to be pathogenic (PMID: 14647210, 18182601, 21769658, 24156927, 25330149; Invitae). This suggests that this variant may also be clinically significant and likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The BRCA2 c.67+3A>G variant was identified in the literature in an Australian patient with bilateral breast cancer who had a strong family history of cancer (sister with endometrial cancer, mother with breast cancer, maternal grandmother with an unknown cancer type) (Parsons_2015_PMID:24302565). This variant was also reported in a compound heterozygous proband with Fanconi anaemia and leukemia who died at 17 months; the BRCA2 c.67+3A>G variant was inherited from the unaffected mother and the proband's second BRCA2 variant (p.I924Rfs*38) was inherited from the unaffected father (Feben_2017_PMID:28185119). The variant was identified in dbSNP (ID: rs1593880835) and ClinVar (classified as likely pathogenic by Ambry Genetics for hereditary cancer-predisposing syndrome). The variant was not identified in the COSMIC database or in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, or the Genome Aggregation Database (March 6, 2019, v2.1.1). The c.67+3A>G variant is located in the 5' splice region but does not affect the invariant +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition, in silico or computational prediction software programs (Splice AI exome, Splice AI genome, dbscSNV Ada, RF) predict deleterious effect on splicing. Further, through in vitro mRNA analysis the c.67+3A>G variant was found to result in exon 2 skipping, resulting in the loss of the consensus ATG start site (Parsons_2015_PMID:24302565). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.