Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PVS1PM2PP3_StrongPP5_Very_Strong
The NM_007294.4(BRCA1):c.5333-1G>T variant causes a splice acceptor 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 22 ACMG points.
PVS1
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PVS1 - null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease
Splicing variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
PM2
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PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
PP3
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PP3 - Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
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PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-43049195-C-A is Pathogenic according to our data. Variant chr17-43049195-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 267600.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43049195-C-A is described in Lovd as [Pathogenic].
The c.5333-1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide upstream from coding exon 20 of the BRCA1 gene. This alteration has been reported in individuals with both early onset and bilateral breast cancers (Wappenschmidt B et al. PLoS ONE, 2012 Dec;7:e50800). Further, a functional analysis by Wappenschmidt et al using patient RNA has shown this alteration results in protein truncation. 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. -
Pathogenic, criteria provided, single submitter
clinical testing
Color Diagnostics, LLC DBA Color Health
Feb 08, 2022
This variant causes a G to T nucleotide substitution at the -1 position of intron 20 of the BRCA1 gene. This variant is also known as IVS21-G>T based on Breast Cancer Information Core (BIC) nomenclature. Functional RNA studies have shown that this variant can cause exon skipping, and is predicted to result in the premature truncation of the protein (PMID: 23239986). This variant has also been reported to be loss-of-function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in individuals affected with breast cancer (PMID: 23239986), and has been identified in one family among the CIMBA participants (PMID: 29446198) (https://cimba.ccge.medschl.cam.ac.uk/). Different variants affecting the same splice acceptor site, c.5333-1G>C and c.5333-1G>A, are known to be disease-causing (ClinVar variation ID: 55534, 55533). This variant has not been identified 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. -
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:1Other:1
not provided, no classification provided
in vitro
Brotman Baty Institute, University of Washington
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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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Neoplasm of ovary Pathogenic:1
Likely pathogenic, no assertion criteria provided
research
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne
Dec 01, 2018
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Hereditary breast ovarian cancer syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter
clinical testing
Invitae
Feb 06, 2021
For these reasons, this variant has been classified as Pathogenic. Studies have shown that this variant is associated with skipping of exon 22, which introduces a premature termination codon (PMID: 23239986). The resulting mRNA is expected to undergo nonsense-mediated decay. Experimental studies have shown that this variant affects BRCA1 protein function (PMID: 30209399). This variant has been observed in individual(s) with breast cancer (PMID: 23239986). ClinVar contains an entry for this variant (Variation ID: 267600). This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 20 of the BRCA1 gene. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. -