Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PVS1PM2PP3_StrongPP5_Very_Strong
The NM_007294.4(BRCA1):c.5333-1G>A 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 Likely 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
?
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-T is Pathogenic according to our data. Variant chr17-43049195-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 55533.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43049195-C-T is described in Lovd as [Likely_pathogenic]. Variant chr17-43049195-C-T is described in Lovd as [Pathogenic].
The c.5333-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 20 of the BRCA1 gene. This alteration has been shown to result in a transcript lacking coding exon 20 (total exon 21) in RNA studies (Ambry internal data; Aspessos A. et al. Cancer Genet 2018 01;220:1-12). This transcript is not expected to trigger nonsense-mediated mRNA decay, however, the impacted region is critical for protein function (Ambry internal data). In addition, 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;562:217-222). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Hereditary breast ovarian cancer syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter
clinical testing
Invitae
Nov 09, 2020
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this variant disrupts mRNA splicing and is expected to lead to the loss of protein expression (30209399, 29310832). This variant has been observed in individuals affected with breast cancer (PMID: 19941162, 29310832, 28294317). This variant is also known as IVS21-1G>A in the literature. ClinVar contains an entry for this variant (Variation ID: 55533). 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. -