Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_007294.4(BRCA1):c.5332+1G>A variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000000684 in 1,461,614 control chromosomes in the GnomAD database, with no homozygous occurrence. 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, No cryptic splice site detected. Exon removal results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-43051062-C-T is Pathogenic according to our data. Variant chr17-43051062-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 55527.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43051062-C-T is described in Lovd as [Pathogenic]. Variant chr17-43051062-C-T is described in Lovd as [Pathogenic]. Variant chr17-43051062-C-T is described in Lovd as [Benign].
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:5Other:1
Pathogenic, criteria provided, single submitter
clinical testing
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge
Oct 02, 2015
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not provided, no classification provided
in vitro
Brotman Baty Institute, University of Washington
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Pathogenic, no assertion criteria provided
clinical testing
Breast Cancer Information Core (BIC) (BRCA1)
Jun 21, 1999
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Pathogenic, criteria provided, single submitter
clinical testing
University of Science and Technology Houari Boumediene, Laboratory of Molecular and Cellular Biology (LBCM)
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Pathogenic, reviewed by expert panel
curation
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Apr 03, 2016
Allele-specific assay on patient-derived mRNA demonstrated that the variant allele produces only predicted non-functional transcripts. Variant allele produces r.5278_5332del transcript (encoding predicted non-functional protein). -
Pathogenic, criteria provided, single submitter
clinical testing
Baylor Genetics
Jun 26, 2023
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not provided Pathogenic:3
Pathogenic, no assertion criteria provided
clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
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Pathogenic, criteria provided, single submitter
clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano
Oct 03, 2016
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Pathogenic, no assertion criteria provided
clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
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Hereditary breast ovarian cancer syndrome Pathogenic:3
Pathogenic, criteria provided, single submitter
clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Jul 26, 2022
Variant summary: BRCA1 c.5332+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 5 splicing donor site. Experimental evidence supports these predictions demonstrating that this variant affects mRNA splicing, leading to skipping of exon 20 (Colombo_2013). The variant allele was found at a frequency of 4e-06 in 251352 control chromosomes (gnomAD). c.5332+1G>A has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (e.g. Rebbeck_2018). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function through employment of a cell-survival assay in a population of edited haploid HAP1 cells as a measure of functional HDR pathway, determined the variant to be non-functional (Findlay_2018). Seven 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
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State
Nov 16, 2021
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Pathogenic, criteria provided, single submitter
clinical testing
Labcorp Genetics (formerly Invitae), Labcorp
Jun 26, 2022
ClinVar contains an entry for this variant (Variation ID: 55527). This variant is also known as c.5451+1G>A. Disruption of this splice site has been observed in individual(s) with breast and/or ovarian cancer (PMID: 11084537, 16324400, 19629752, 27083178). This variant is present in population databases (rs80358041, gnomAD 0.006%). This sequence change affects a donor splice site in intron 20 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. Studies have shown that disruption of this splice site results in skipping of exon 20 (also known as exon 21) and introduces a premature termination codon (PMID: 23451180, 24667779; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
This variant causes a G to A nucleotide substitution at the +1 position of intron 20 of the BRCA1 gene. RNA studies have reported that this variant causes the out-of-frame skipping of exon 20 resulting in premature termination (PMID: 19629752, 24667779) and a functional study has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in at least five individuals affected with breast or ovarian cancer (PMID: 19629752, 26541979, 26997744, 27083178, 28993434, 30715675, 33471991, 35464868; Leiden Open Variation Database DB-ID BRCA1_000567). This variant has been identified in 1/251352 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. -
Pathogenic, criteria provided, single submitter
clinical testing
Ambry Genetics
Jun 29, 2021
The c.5332+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 19 of the BRCA1 gene. This mutation was found to be de novo in a female diagnosed with bilateral breast cancers at ages 38 and 43 (Edwards E et al. Fam. Cancer. 2009; 8(4):479-82) and has also been reported in a Chinese female with ovarian cancer (Hasmad HN et al. Gynecol. Oncol. 2015 Nov) and in an Algerian female diagnosed with triple negative breast cancer at age 34 (Henouda S et al. Dis. Markers 2016; Epub 2016 Feb 22). RNA splicing assays have shown this alteration to cause coding exon 19 (exon 21 in literature) skipping (Ambry internal data; Colombo M et al. PLoS ONE. 2013; 8(2): e57173; Steffensen AY et al. Eur. J. Hum. Genet. 2014 Dec;22:1362-8). One functional study found that this nucleotide substitution is deleterious in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature 2018 10;562(7726):217-222). 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. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -