Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_007294.4(BRCA1):c.5468-2A>G 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 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 18 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease,
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-43045804-T-C is Pathogenic according to our data. Variant chr17-43045804-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 91653.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43045804-T-C is described in Lovd as [Pathogenic].
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:4Other:1
Likely pathogenic, no assertion criteria provided
clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System
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The BRCA1 c.5468-2A>G variant was identified in 3 of 83182 proband chromosomes (frequency: 0.00004) from individuals or families with breast or ovarian cancer (Golmard 2016, Rebbeck 2018). The variant was also identified in dbSNP (ID: rs398122699) as "With Pathogenic, other allele", in ClinVar (classified as pathogenic by CIMBA; as likely pathogenic by Invitae and SCRP), and in LOVD 3.0 (2x as pathogenic). The variant was not identified in UMD-LSDB, database. The variant was not identified in the Genome Aggregation Database (Feb 27, 2017). The c.5468-2A>G variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic. -
Likely pathogenic, no assertion criteria provided
clinical testing
Sharing Clinical Reports Project (SCRP)
Nov 09, 2009
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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
Likely pathogenic, criteria provided, single submitter
clinical testing
Ambry Genetics
Mar 19, 2020
The c.5468-2A>G intronic variant results from an A to G substitution two nucleotides upstream from coding exon 22 in the BRCA1 gene. This alteration has been reported in multiple individuals from a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations (Rebbeck TR et al. Hum. Mutat., 2018 May;39:593-620). It has also been reported as a de novo alteration in an individual with ovarian cancer at age 39, however it is it unclear if paternity was confirmed in this study (Golmard L et al. Oncogene, 2016 Mar;35:1324-7). 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). A close match alteration at this acceptor site, BRCA1 c.5468-1G>A was shown to make use of a cryptic acceptor site 11nt downstream (Baert A et al. Hum. Mutat., 2018 04;39:515-526). This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice acceptor site; however, direct evidence is insufficient at this time (Ambry internal data). Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein. As such, this alteration is classified as likely pathogenic. -
Hereditary breast ovarian cancer syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter
clinical testing
Labcorp Genetics (formerly Invitae), Labcorp
Sep 27, 2022
Disruption of this splice site has been observed in individual(s) with hereditary breast and ovarian cancer syndrome (PMID: 26028024). In at least one individual the variant was observed to be de novo. For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 91653). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 22 of the BRCA1 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. -