Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_007294.4(BRCA1):c.302-1G>C variant causes a splice acceptor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).
BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 3.3, offset of 10, new splice context is: tattttacacatgcaaacAGcta. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-43104262-C-G is Pathogenic according to our data. Variant chr17-43104262-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 54751.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43104262-C-G is described in Lovd as [Pathogenic].
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:2
Pathogenic, no assertion criteria provided
research
Centro de Genética y Biología Molecular, Universidad de San Martín de Porres
Jul 15, 2015
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Pathogenic, reviewed by expert panel
curation
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Aug 10, 2015
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 = 1 -
This variant causes a G to C nucleotide substitution at the -1 position of intron 5 of the BRCA1 gene. RNA studies have shown that this variant causes out-of-frame skipping of exon 6, resulting in premature truncation (PMID: 28944232). This variant has been reported in individuals affected with breast cancer (PMID: 16267036, 28944232; Color internal data). In a Peruvian family affected with multiple cases of breast and ovarian cancer, this variant was reported in the proband and two first-degree cousins with breast cancer (PMID: 28944232). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). A multifactorial analysis has reported a family history likelihood ratio for pathogenicity of 1.84 (PMID: 17924331). Loss of BRCA1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter
clinical testing
Ambry Genetics
Sep 06, 2023
The c.302-1G>C intronic variant results from a G to C substitution one nucleotide upstream from coding exon 5 of the BRCA1 gene. Also designated as IVS6-1G>C, this alteration has been reported in several breast and/or ovarian cancer cohorts (Judkins T et al. Cancer Res, 2005 Nov;65:10096-103; Buleje J et al. Mol Genet Genomic Med, 2017 Sep;5:481-494; Eoh KJ et al. Cancer Res Treat, 2018 Jul;50:917-925; Park JS et al. Clin Breast Cancer, 2018 10;18:362-373.e1; Laitman Y et al. Hum Mutat, 2019 11;40:e1-e23; Herzog JS et al. NPJ Breast Cancer. 2021 Aug;7(1):107). This alteration was classified as pathogenic by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, and mutation co-occurrence (Easton DF et al. Am J Hum Genet, 2007 Nov;81:873-83; Lindor NM et al. Hum Mutat, 2012 Jan;33:8-21). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). As such, this alteration is classified as likely pathogenic. -
Hereditary breast ovarian cancer syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter
clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Jul 29, 2019
Variant summary: BRCA1 c.302-1G>C 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 3' acceptor site. Experimental evidence support these predictions demonstrating this variant to generate a transcript lacking exon 7, with the inclusion of seven new amino acids in the BRCA1 protein and the appearance of premature stop codon in position 148 (p.Q141EfsX8) (Buleje_2017). The variant was absent in 250608 control chromosomes (gnomAD). c.302-1G>C has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer (Buleje_2017, Eoh_2018, Park_2018). These data indicate that the variant is very likely to be associated with disease. Two ClinVar submitters including an expert panel (ENIGMA) (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter
clinical testing
Labcorp Genetics (formerly Invitae), Labcorp
Oct 29, 2018
For these reasons, this variant has been classified as Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BRCA1 are known to be pathogenic (PMID: 20104584). Based on a multifactorial likelihood algorithm using genetic and clinical data, this variant has been determined to have a high probability of being pathogenic (PMID: 17924331, 21990134). This variant has been observed to segregate with breast cancer in an affected family (PMID: 28944232). This variant is also known as IVS6-1G>C in the literature. ClinVar contains an entry for this variant (Variation ID: 54751). This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 5 of the BRCA1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. Experimental studies have shown that this intronic change leads to skipping of exon 6 (referred to as exon 7 in the paper) and creates a premature stop codon (PMID: 28944232). -