Our verdict is Uncertain significance. The variant received 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_007294.4(BRCA1):c.5333-6T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
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]
BRCA1 Gene-Disease associations (from GenCC):
breast-ovarian cancer, familial, susceptibility to, 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-43049200-A-C is Pathogenic according to our data. Variant chr17-43049200-A-C is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 55538.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01). . Strength limited to SUPPORTING due to the PP5.
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
The BRCA1 c.5333-6T>G variant has been reported in the published literature in an individual with a personal and/or family history of breast and ovarian cancer (PMID: 11802209 (2002)). It was also reported to result in exon 22 skipping (PMID: 31131967 (2019)), as well as being non-functional using a saturation genome editing assay (PMID: 30209399 (2018)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper BRCA1 mRNA splicing (Alamut Visual (http://www.interactive-biosoftware.com/). Based on the available information, we are unable to determine the clinical significance of this variant. -
Jun 13, 2024
Mayo Clinic Laboratories, Mayo Clinic
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
PP4, PM2, PS3 -
Breast-ovarian cancer, familial, susceptibility to, 1Pathogenic:2
Jan 08, 2024
All of Us Research Program, National Institutes of Health
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This variant causes a T to G nucleotide substitution at the -6 position of intron 20 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. An RNA study has reported that this variant causes the out-of-frame skipping of exon 21 (PMID: 11802209) and this variant also has been reported in ClinVar to cause abnormal splicing (SCV002646843.1). A functional assay that required proper splicing for the measured activity has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). Since this variant does not directly impact the coding sequence, the splicing prediction, RNA data and functional data could be interpreted together as evidence for a significant disruption in RNA processing. This variant has been detected in an individual affected with breast cancer and reported in two families affected with breast cancer and both breast and ovarian cancer (PMID: 11802209; Color internal data). A multifactorial analysis has reported likelihood ratios for pathogenicity based on segregation and tumor pathology of 0.6846 and 3.73, respectively (PMID: 31131967). 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 Likely Pathogenic. -
The c.5333-6T>G intronic pathogenic mutation results from a T to G substitution 6 nucleotides upstream from coding exon 20 in the BRCA1 gene. This nucleotide position is well conserved in available vertebrate species. This alteration was detected in 1/989 unrelated individuals from a cohort of German breast and/or ovarian cancer families (Meindl A et al. Int. J. Cancer. 2002 Feb;97:472-80). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data; Meindl A et al. Int. J. Cancer. 2002 Feb;97:472-80). One study found that this nucleotide substitution is non-functional in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature. 2018 10;562:217-222). In addition, was called likely pathogenic based on multifactorial likelihood analysis (Parsons MT et al. Hum. Mutat. 2019 09;40:1557-1578). In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Nov 16, 2023
Color Diagnostics, LLC DBA Color Health
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This variant causes a T to G nucleotide substitution at the -6 position of intron 20 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. An RNA study has reported that this variant causes the out-of-frame skipping of exon 21 (PMID: 11802209) and this variant also has been reported in ClinVar to cause abnormal splicing (SCV002646843.1). A functional assay that required proper splicing for the measured activity has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). Since this variant does not directly impact the coding sequence, the splicing prediction, RNA data and functional data could be interpreted together as evidence for a significant disruption in RNA processing. This variant has been detected in an individual affected with breast cancer and reported in two families affected with breast cancer and both breast and ovarian cancer (PMID: 11802209; Color internal data). A multifactorial analysis has reported likelihood ratios for pathogenicity based on segregation and tumor pathology of 0.6846 and 3.73, respectively (PMID: 31131967). 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 Likely Pathogenic. -
Hereditary breast ovarian cancer syndromePathogenic:1
Oct 16, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This sequence change falls in intron 20 of the BRCA1 gene. It does not directly change the encoded amino acid sequence of the BRCA1 protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with a personal and/or family history of breast and ovarian cancer (PMID: 11802209). This variant is also known as IVS21-6T>G. ClinVar contains an entry for this variant (Variation ID: 55538). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects BRCA1 function (PMID: 30209399). Studies have shown that this variant results in skipping of exon 21 and introduces a new termination codon (internal data). However the mRNA is not expected to undergo nonsense-mediated decay. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Familial cancer of breastOther:1
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ClinVar Staff, National Center for Biotechnology Information (NCBI)