ClinVar Genomic variation as it relates to human health

This variant causes a G to A nucleotide substitution at the -1 position of intron 13 splice acceptor site of the BRCA1 gene. A functional RNA study has shown that this variant results in the production of two different mutant transcripts: one due to the use of a cryptic acceptor site at c.4513 in exon 15, causing a deletion of 29 basepairs and premature protein truncation at codon 1496; and the other due to out-of-frame skipping of exon 14 (exon 15 according to BIC exon nomenclature), causing premature protein truncation at codon (PMID: 31843900). These transcripts are expected to result in a loss of BRCA1 function. This variant has been reported in multiple individuals affected with hereditary breast and/or ovarian cancer and is a recurrent mutation in the Pakistani individuals (PMID: 12181777, 27553291, 31843900). This variant has been identified in 3/251076 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

Variant summary: BRCA1 c.4485-1G>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: Four predict the variant abolishes a canonical 3 acceptor site and creates a new cryptic exonic one. Experimental evidence supports these predictions demonstrating that this variant affects mRNA splicing, leading to aberrant transcripts and premature termination codons (Casadei_2019). The variant allele was found at a frequency of 1.2e-05 in 251076 control chromosomes (gnomAD). c.4485-1G>A has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (e.g. Liede_2002, Malik_2009, Casadei_2019). These data indicate that the variant is very likely to be associated with disease. Nine ClinVar submitters (evaluation after 2014) cite the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change affects an acceptor splice site in intron 13 of the BRCA1 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 present in population databases (rs80358189, gnomAD 0.01%). Disruption of this splice site has been observed in individual(s) with breast and/or ovarian cancer (PMID: 12181777, 27553291, 29446198, 31528241, 31843900, 35377489). This variant is also known as IVS14-1G>A. ClinVar contains an entry for this variant (Variation ID: 55213). Studies have shown that disruption of this splice site results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 31843900; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

Canonical splice site variant demonstrated to result in aberrant splicing, leading to a null allele in a gene for which loss of function is a known mechanism of disease (PMID: 31843900); Not observed at significant frequency in large population cohorts (gnomAD); Also known as IVS14-1G>A; This variant is associated with the following publications: (PMID: 15533909, 25525159, 21559243, 12181777, 35693198, 31528241, 38355628, 29922827, 29446198, 35377489, 37306523, 38575974, 35216584, 35000471, 31843900, 27553291, 35710434)

The c.4485-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 13 of the BRCA1 gene. This alteration has been reported in Pakistani families with breast and/or ovarian cancer (Liede A et al. Am. J. Hum. Genet., 2002 Sep;71:595-606; Rashid MU et al. BMC Cancer, 2016 08;16:673). 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 BRCA1, c.4485-1G>A variant was identified in 4 of 922 proband chromosomes (frequency: 0.004) from individuals or families with hereditary breast and ovarian cancer and was not identified in 200 control chromosomes from healthy individuals (Liede 2002); however, an insufficient number of controls were included in these studies to determine the frequency of this variant in the general population. The mutation was found in multiple case subjects and represents a candidate founder mutation in the Pakistani population (Liede 2002). The variant was also identified in dbSNP (ID: rs80358189) “With Pathogenic allele”, HGMD as a “disease causing mutation”, the ClinVar database (classified as a pathogenic variant by the Sharing Clinical Reports Project, derived from Myriad reports), the BIC database (2X with “pending” clinical importance), and UMD (3X as a causal variant). The c.4485-1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) 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.