Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_007294.4(BRCA1):c.301+6T>C variant causes a splice region, intron change. The variant allele was found at a frequency of 0.00000685 in 1,459,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to 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]
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:1Uncertain:3Benign:1Other:1
Mar 25, 2024
Baylor Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
-
Brotman Baty Institute, University of Washington
Significance: not provided
Review Status: no classification provided
Collection Method: in vitro
- -
Apr 07, 2024
St. Jude Molecular Pathology, St. Jude Children's Research Hospital
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
The BRCA1 c.301+6T>C intronic change results in a T to C substitution at the +6 position of intron 5 of the BRCA1 gene. Algorithms that predict the impact of sequence changes on splicing indicate that this change may impact splicing. A published RNA study reports this variant is associated with very low levels of aberrant transcript (PMID: 21769658). This variant has a maximum subpopulation frequency of 0.002% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). This variant has been reported in individuals with breast and/or ovarian cancer (PMID: 21769658, 26845104). In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.? -
Apr 12, 2024
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: curation
Each variant was annotated with functional scores from MAVE data which was translated into functional evidence codes. All other evidence codes and combining criteria were adhered to as closely as possible based on the ClinGen VCEP (Variant Curation Expert Panel) gene-specific recommendations. See Supplemental Figure 34 of final paper (Supp Fig. 28 in preprint: doi:10.1101/2024.04.11.24305690) for a table to see which lines of evidence we did not have data for. The ClinGen VCEPs are highly regarded as the gold-standard for gene-specific variant curation and are developed after extensive evaluation of the evidence by clinical and scientific experts for the particular gene to classify genomic variants on a spectrum from pathogenic to benign using the 2015 ACMG/AMP Variant Interpretation Guidelines as a backbone (PMID: 25741868). Reclassification of these VUS variants from gnomAD or All of Us focused only on variants originally prescribed as VUS in ClinVar. To ensure reproducibility, transparency, and increased throughput, all the procedures for annotating variants and assigning evidence codes were codified using Python. All code has been made freely available and is linked in the Code Availability section and all reclassified variants with evidence codes used can be found in Tables S18-19 (preprint: doi:10.1101/2024.04.11.24305690). For the MAVE data, the clinical curation and clinical strength assignment as per the ClinGen recommendations in Brnich et al. (2020) (PMID: 31892348) for or against pathogenicity or benignity of each of these MAVE datasets utilized in this study were previously published in Fayer et al. (2021) (PMID: 34793697).In brief, for BRCA1 variants, if a variant was categorized as FUNC (functional), it was assigned BS3 evidence and no PS3 evidence, whereas if it was categorized as LOF (loss of function), the variant was assigned PS3 evidence and no BS3 evidence. Variants categorized as INT (intermediate) were left unannotated. For the BRCA1 combining criteria, greater than or equal to 1 criteria of strong benign evidence was enough to reclassify the VUS as Likely Benign. This variant GRCh38:17:43104862:A>G was assigned evidence codes ['PS3', 'PP3', 'PM2_Supporting'] and an overall classification of Likely pathogenic -
Nov 20, 2015
University of Washington Department of Laboratory Medicine, University of Washington
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Sep 01, 2023
Department of Medical and Surgical Sciences, University of Bologna
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
PM2(Supporting)+PP3(Supporting)+BS3(Strong)+BP5(Very Strong) according to ACMG/AMP classification guidelines specified for BRCA1 & BRCA2 (Classification Criteria V1.0.0 2023-09-08 - https://cspec.genome.network/cspec/ui/svi/affiliation/50087) (PMID: 38160042) -
not provided Uncertain:2
Apr 23, 2024
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
The BRCA1 c.301+6T>C variant has been reported in the published literature in individuals with breast cancer (PMIDs: 34178674 (2021), 21769658 (2012)) and ovarian cancer (PMID: 26845104 (2016)). Experimental studies indicate this variant causes low levels of aberrant splicing (PMID: 21769658 (2012)), and is described as being non-functional in a DNA repair-dependent cell survival assay (PMID: 30209399 (2018)). The frequency of this variant in the general population, 0.000012 (3/251174 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on BRCA1 mRNA splicing yielded inconclusive findings. Based on the available information, we are unable to determine the clinical significance of this variant. -
Dec 12, 2023
GeneDx
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
Observed in individuals with a personal or family history of breast and/or ovarian cancer (PMID: 21769658, 26845104, 34178674); Published functional studies are conflicting: variant classified as non-functional based on a saturation genome editing (SGE) assay measuring cell survival (PMID: 30209399); an RNA study detected very low levels of aberrant transcript predicted to encode an in-frame change of four amino acids (p.Gly98_Tyr101delinsAsp); however, multifactorial likelihood analysis incorporating these splicing data resulted in classification of this variant as not pathogenic/low clinical significance (PMID: 21769658); Classified as benign (IARC class 1) in one multi-factorial likelihood assessment utilizing co-segregation, family history, and co-occurrence data, but specific clinical details were not provided (PMID: 34597585); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Also known as IVS6+6T>C and 420+6T>C; This variant is associated with the following publications: (PMID: 26913838, 26845104, 21769658, 34178674, 29750258, 23893897, 20858050, 30209399, Findlay2023[interimreport], 34597585) -
Review Status: criteria provided, single submitter
Collection Method: clinical testing
This variant causes a T to C nucleotide substitution at the +6 position of intron 5 of the BRCA1 gene. An RNA study has reported a very low level of aberrant splicing product lacking the last nine nucleotides of exon 5 predicted to result in an in-frame deletion of three amino acids (PMID: 21769658). A functional study has reported that this variant disrupts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in two individuals affected with breast or ovarian cancer (PMID: 21769658, 26845104). This variant has been identified in 3/251174 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Oct 29, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
The c.301+6T>C intronic alteration consists of a T to C substitution nucleotides after coding exon 4 in the BRCA1 gene. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not specified Uncertain:1
Jan 31, 2019
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
Variant summary: BRCA1 c.301+6T>C alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant weakens a 5' donor site. One predicts that the variant abolishes a 5' splicing donor site. This is supoprted by a study reporting very low levels of aberrant transcript, possibly resulting from use of a cryptic site at c.292, 9 nucleotides upstream from canonical 5' splice donor site (Thomassen_2011). The variant allele was found at a frequency of 1.2e-05 in 245948 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.301+6T>C has been reported in the literature in an individual affected with ovary cancer (Shirts_2015) and in an individual affected with breast cancer and with a family history of breast and ovarian cancer and other cancers including lung cancer, layrynx cancer and myeloma however, without evidence of co-segregation of the variant with disease (Thomassen_2011). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. Experimental evidence evaluating an impact on protein function through assessment of functional homology-directed DNA repair (HDR) pathway reported the variant with a functional score supporting loss of function (Findlay_2018). Four ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Familial cancer of breast;C2676676:Breast-ovarian cancer, familial, susceptibility to, 1;C3280442:Pancreatic cancer, susceptibility to, 4;C4554406:Fanconi anemia, complementation group S Uncertain:1
Mar 16, 2022
Fulgent Genetics, Fulgent Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Hereditary breast ovarian cancer syndrome Uncertain:1
Dec 24, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
This sequence change falls in intron 5 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 results in the loss of 3 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs753859240, gnomAD 0.002%). This variant has been observed in individual(s) with breast cancer and ovarian cancer (PMID: 21769658, 26845104, 34178674). ClinVar contains an entry for this variant (Variation ID: 224562). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a low probability of being pathogenic (PMID: 21769658). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in the activation of a cryptic splice site in exon 5 (PMID: 21769658; internal data). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -