Submissions for variant NM_007294.4(BRCA1):c.5332+4A>G

gnomAD frequency: 0.00002  dbSNP: rs80358166

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000131936	SCV000186992	uncertain significance	Hereditary cancer-predisposing syndrome	2024-05-31	criteria provided, single submitter	clinical testing	The c.5332+4A>G intronic variant results from an A to G substitution 4 nucleotides after coding exon 19 in the BRCA1 gene. This nucleotide position is highly conserved in available vertebrate species. This alteration has been found in multiple breast and/or ovarian cancer cohorts (Lecarpentier J et al. Breast Cancer Res. 2012 Jul;14:R99; Rebbeck TR et al. Hum. Mutat. 2018 05;39:593-620). RNA studies have demonstrated that this alteration results in an incomplete splice defect of CDS19 skipping (also referred to as exon 20 in the literature); the clinical impact of this abnormal splicing is unknown at this time (Wangensteen T et al. Hered Cancer Clin Pract. 2019 May;17:14; Ambry internal data); This nucleotide substitution is functional in a high throughput genome editing haploid cell survival assay that can measure both protein and mRNA effects (Findlay GM et al. Nature. 2018 10;562:217-222). In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Based on the available evidence, the clinical significance of this variant remains unclear.
GeneDx	RCV000160005	SCV000210216	uncertain significance	not provided	2014-07-16	criteria provided, single submitter	clinical testing	This variant is denoted BRCA1 c.5332+4A>G or IVS20+4A>G and consists of an A>G nucleotide substitution at the +4 position of intron 20 of the BRCA1 gene. Multiple in silico models predict this variant to weaken the nearby natural donor site, and to possibly cause abnormal gene splicing. This variant, also known as IVS21+4A>G using alternate nomenclature, has been observed in an individual with a history suggestive of Hereditary Breast and Ovarian Cancer syndrome (Lecarpentier 2012) BRCA1 c.5332+4A>G was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The adenine (A) nucleotide that is altered is well conserved across species. Based on currently available information, it is unclear whether BRCA1 c.5332+4A>G is pathogenic or benign. We consider it to be a variant of uncertain significance.
Color Diagnostics, LLC DBA Color Health	RCV000131936	SCV000908982	uncertain significance	Hereditary cancer-predisposing syndrome	2023-08-14	criteria provided, single submitter	clinical testing	This variant causes an A to G nucleotide substitution at the +4 position of intron 20 of the BRCA1 gene. This variant is also known as IVS21+4A>G according to the BIC nomenclature. Splice prediction tools suggest that this variant is unlikely to affect splicing. An RT-PCR study using RNA derived from a carrier individual has reported that this variant may cause out-of-frame skipping of exon 20 (PMID: 31143303). However, the study did not show if the aberration was complete or partial and was unable to draw any conclusion about pathogenicity of this variant. A functional study that requires splicing of variant transcript has reported that this variant does not impact BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in an individual affected with or at risk of breast cancer (PMID: 22762150). This variant has been identified in 4/251334 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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000807389	SCV000947437	uncertain significance	Hereditary breast ovarian cancer syndrome	2025-01-21	criteria provided, single submitter	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 may result in an absent or altered protein product. This variant is present in population databases (rs80358166, gnomAD 0.01%). This variant has been observed in individual(s) with clinical features of hereditary breast and/or ovarian cancer syndrome (PMID: 22762150, 29446198, 34981296). This variant is also known as IVS21+4A>G. ClinVar contains an entry for this variant (Variation ID: 125827). 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 skipping of exon 20, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 30209399; 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.
Baylor Genetics	RCV000112618	SCV004216831	likely pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2023-02-16	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000112618	SCV004832259	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 1	2023-12-15	criteria provided, single submitter	clinical testing	This variant causes an A to G nucleotide substitution at the +4 position of intron 20 of the BRCA1 gene. This variant is also known as IVS21+4A>G according to the BIC nomenclature. Splice prediction tools suggest that this variant is unlikely to affect splicing. An RT-PCR study using RNA derived from a carrier individual has reported that this variant may cause out-of-frame skipping of exon 20 (PMID: 31143303). However, the study did not show if the aberration was complete or partial and was unable to draw any conclusion about pathogenicity of this variant. A functional study that requires splicing of variant transcript has reported that this variant does not impact BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in an individual affected with or at risk of breast cancer (PMID: 22762150). This variant has been identified in 4/251334 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.
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine	RCV000112618	SCV005402639	likely benign	Breast-ovarian cancer, familial, susceptibility to, 1	2024-04-12	criteria provided, single submitter	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 GRCh38:17:43051059:T>C was assigned evidence codes ['BS3'] and an overall classification of Likely benign
Breast Cancer Information Core (BIC) (BRCA1)	RCV000112618	SCV000145460	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 1	2004-11-25	no assertion criteria provided	clinical testing
Brotman Baty Institute, University of Washington	RCV000112618	SCV001238144	not provided	Breast-ovarian cancer, familial, susceptibility to, 1		no assertion provided	in vitro
BRCAlab, Lund University	RCV000112618	SCV004243921	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 1	2020-03-02	no assertion criteria provided	clinical testing