ClinVar Genomic variation as it relates to human health

IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 0.999853

The c.632-1G>A intronic variant results from a G to A substitution one nucleotide upstream from coding exon 7 of the BRCA2 gene. This alteration has been reported in several BRCA1/2 positive cohorts (Al-Mulla F et al. J. Clin. Pathol., 2009 Apr;62:350-6; Edwards SM et al. Br. J. Cancer, 2010 Sep;103:918-24; Rebbeck TR et al. Hum. Mutat., 2018 05;39:593-620). This alteration is also reported as c.860-1G>A 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 likely pathogenic.

Disruption of this splice site has been observed in individual(s) with breast, ovarian or prostate cancer (PMID: 20736950, 29371908, 29446198). For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in skipping of exon 8 and introduces a premature termination codon (PMID: 18819001). The resulting mRNA is expected to undergo nonsense-mediated decay. 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: 31131967). ClinVar contains an entry for this variant (Variation ID: 52060). This variant is also known as c.860-1G>A. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 7 of the BRCA2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.

The BRCA2 c.632-1G>A variant was identified in 7 of 74942 proband chromosomes (frequency: 0.000093) from Japanese, Caucasian, Asian and U.K. individuals or families with familial breast cancer or prostate cancer and was not identified in 22482 control chromosomes from healthy individuals (Tesoriero 2005, Rebbeck 2018, Momozawa 2018). The variant was also identified in dbSNP (ID: rs81002820) as "With Likely pathogenic, Pathogenic allele ", ClinVar (classified as pathogenic by the University of Cambridge and Mount Sinai Hospital (Toronto), and LOVD 3.0 (classified as pathogenic by 4 submitters). The variant was not identified in UMD-LSDB. The variant was also identified by our laboratory in 1 individual with breast cancer. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). In a study of 720 familial breast cancer families, this variant was identified in 3 families (Tesoriero 2005). In this paper this variant was predicted to result in the deletion of exon 8 by disrupting the intron 7 acceptor site. RT-PCR of BRCA2, c.632-1G>A RNA was undertaken and the entire RT-PCR reaction was cloned and sequenced. Of the fifty clones sequenced, only the wildtype transcript and a transcript lacking exon 8 (BRCA2, c.860_909del) were identified. No other alternative transcripts were found. The resulting BRCA2 c.860-909del introduces a frameshift that is predicted to create a stop at codon 220, and the authors therefore considered this variant to be pathogenic. The c.632-1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence and 4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.