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 = 0.999891

Variant summary: The BRCA2 c.8755-1G>A variant involves the alteration of a conserved intronic nucleotide and 3/5 splice prediction tools predict a significant impact on normal splicing. A functional study, Colombo_2013, shows the variant to produce two aberrant transcripts, skipping of exon 22 (resulting in p.Gly2919LeufsX3) and skipping of exon 22 + 51 bp at the 5' end of exon 23 (resulting in p.Gly2919LysfsX26). This variant is absent in 244786 control chromosomes (gnomAD). A publication, Tea_2014, reports the variant in 26 affected individuals from 13 families. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "Pathogenic." Taken together, this variant is classified as pathogenic.

This c.8755-1G>A variant in the BRCA2 gene has been shown to alter mRNA splicing and is predicted to introduce a premature translation termination codon (PMID 18489799, 23451180, 25382762). This variant has been reported in multiple families affected with hereditary breast and ovarian cancer (PMID 18489799, 24156927) and has never been observed in general population databases. Therefore, the c.8755-1G>A variant is classified as pathogenic.

Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Wagner et al., 1999; Tea et al., 2014; Lerner-Ellis et al., 2021; Solao et al., 2021); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 8983-1G>A; This variant is associated with the following publications: (PMID: 23199084, 31131967, 29785153, 23451180, 9971877, 18489799, 25382762, 24156927, 23772696, 27060066, 20104584, 28726806, 29360161, 30257646, 29387975, 29446198, 29922827, 28918466, 32206145, 32885271, 32438681, 35264596, 24312913, 34072659, Eniu2017[Abstract])

The c.8755-1G>A variant in BRCA2 has been reported in at least 10 individuals wi th BRCA2-associated cancers and segregated with disease in 3 affected relatives from 3 families (Wagner 1999, Machackova 2008, Breast Cancer Information Core da tabase, www.research.nhgri.nih.gov/bic/). It was absent from large population st udies. This variant occurs in the invariant region (+/- 1,2) of the splice conse nsus sequence and in vitro studies indicate that this variant results in skippin g of exon 22, leading to a premature stop codon and an abnormal or absent protei n (Machackova 2008, Colombo 2013). Heterozygous loss of function of the BRCA2 ge ne is an established disease mechanism in hereditary breast and ovarian cancer ( HBOC). In summary, this variant meets our criteria to be classified as pathogeni c for HBOC in an autosomal dominant manner based upon the predicted impact to th e protein, segregation studies, and prevalence in affected individuals.

This variant causes a G to A nucleotide substitution at the canonical -1 position of intron 21 splice acceptor site of the BRCA2 gene. This variant is also known as IVS21-1G>A in the literature. Functional RNA studies have shown that this variant causes skipping of exon 22 or skipping of exon 22 plus first 51 nucleotides of exon 23 (PMID: 9971877, 18489799, 23451180, 25382762). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in over fifteen individuals affected with breast and/or ovarian cancer (PMID: 9971877, 11802209, 18489799, 29785153, 32206145, 32438681; Matteis 2019, DOI: 10.12892/ejgo5165.2019) and in an individual affected with pancreatic and prostate cancer with family history of breast and/or ovarian cancer (PMID: 29360161). This variant has also been reported in 26 individuals from 13 different families at high risk for breast cancer (PMID: 24156927). 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 Pathogenic.

PVS1, PS3, PS4_STR, PM2_SUP, PP1

_x000D_ Criteria applied: PVS1, PS3_MOD, PS4_MOD, PM2_SUP

PP5, PM2, PVS1

This sequence change affects an acceptor splice site in intron 21 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. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with personal and/or family history of breast and/or ovarian cancer (PMID: 9971877, 18489799, 24156927). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 38183). Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 9971877, 23451180, 25382762). For these reasons, this variant has been classified as Pathogenic.

The c.8755-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 21 of the BRCA2 gene. This alteration has been identified in multiple individuals with a personal and/or family history of breast and/or ovarian cancer (Machackova E et al. BMC Cancer. 2008 May;8:140; Tea MK et al. Maturitas. 2014 Jan;77:68-72; Goidescu IG et al. Clujul Med, 2018 Apr;91:157-165; Boltear L et al. Hered Cancer Clin Pract, 2020 Mar;18:7). This alteration has also been reported in 1 of 1296 individuals with pancreatic adenocarcinoma (Dudley B et al. Cancer, 2018 Apr;124:1691-1700). In multiple RNA studies, transcript analysis and minigene assays revealed aberrant transcripts that can lead to a frameshift as the result of this alteration (Ambry internal data; Colombo M et al. PLoS ONE. 2013 Mar;8(2):e57173; Acedo A et al. Hum. Mutat. 2015 Feb;36(2):210-21). 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.

The BRCA2 c.8755-1G>A variant was identified in the literature however the frequency of this variant in an affected population was not provided. The variant was also identified in dbSNP (ID: rs81002812) as With Likely pathogenic, Pathogenic allele, ClinVar (classified as pathogenic by Invitae, Ambry Genetics, BIC; classified as likely pathogenic by SCRP, Counsyl; classified as uncertain significance by ENIGMA ), Clinvitae (conflicting interpretations of pathogenicity), Genesight-COGR, LOVD 3.0 , UMD-LSDB (2X causal), BIC Database (6X clinically important), ARUP Laboratories (Definitely pathogenic), databases. The variant was not identified in Zhejiang Colon Cancer Database, databases. The variant was not identified in the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project or the Exome Aggregation Consortium (August 8th 2016) control databases. The c.8755-1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. Several functional studies using splicing assays demonstrated the variant result in aberrant transcripts and considered as deleterious mutations (Acedo 2015, Machackova 2008). mRNA Transcript Analysis in in vitro study by Colombo (2012) showed skipping of exon 22 in one case and skipping of exon 22+51 bp at the 59-end of exon 23 in another. In the same study, cDNA sequence analyses revealed maintenance of the constitutional heterozygosity for c.9876G>A synonymous change (exon 27), indicating expression of the normal mRNA from both the wild-type and mutated alleles. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic.