Submissions for variant NM_007294.4(BRCA1):c.4986+3G>C

dbSNP: rs80358023

Total submissions: 23

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000048721	SCV000076734	pathogenic	Hereditary breast ovarian cancer syndrome	2024-12-13	criteria provided, single submitter	clinical testing	This sequence change falls in intron 15 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 not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast and/or ovarian cancer (PMID: 12491499, 18465347, 23239986, 23772696, 25682074, 25971625, 29446198). This variant is also known as IVS16+3G>C. ClinVar contains an entry for this variant (Variation ID: 55341). 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 activation of a cryptic splice acceptor, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 23239986, 31843900). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics	RCV000162881	SCV000213368	pathogenic	Hereditary cancer-predisposing syndrome	2023-01-10	criteria provided, single submitter	clinical testing	The c.4986+3G>C intronic pathogenic mutation results from a G to C substitution 3 nucleotides after coding exon 14 in the BRCA1 gene. This alteration has been detected in several breast and/or ovarian cancer families as well as in a patient with triple negative breast cancer (Adem C et al. Cancer 2003 Jan; 97(1):1-11; Thomassen M et al. Acta Oncol. 2008;47(4):772-7; Singer CF et al. Clin Genet. 2014 Jan;85(1):72-5; Wong-Brown MW et al. Breast Cancer Res Treat. 2015 Feb;150(1):71-80; Rebbeck TR et al. Hum. Mutat., 2018 May;39:593-620; Dudley B et al. Cancer, 2018 04;124:1691-1700; Carter NJ et al. Gynecol Oncol, 2018 12;151:481-488). 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). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RT-PCR analysis of c.4986+3G>C revealed an alternate transcript with retention of 65 intronic nucleotides resulting in a premature termination codon (Ambry internal data; Wappenschmidt B et al. PLoS ONE 2012; 7(12):e50800). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Of note, this alteration is also designated as IVS16+3G>C in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Counsyl	RCV000112443	SCV000221136	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2015-02-13	criteria provided, single submitter	literature only
GeneDx	RCV000236214	SCV000292524	likely pathogenic	not provided	2018-02-02	criteria provided, single submitter	clinical testing	This variant is denoted BRCA1 c.4986+3G>C or IVS15+3G>C and consists of a G>C nucleotide substitution at the +3 position of intron 15 of the BRCA1 gene. This variant is also known as BRCA1 5105+3G>C or IVS16+3G>C using alternate nomenclature. In vitro RNA analysis demonstrated that this variant causes aberrant splicing, resulting in an out-of-frame intron inclusion predicted to result in protein truncation (Wappenschmidt 2012). This variant has been observed in multiple individuals with a personal and/or family history of breast, ovarian, and/or pancreatic cancer (Adem 2003, Thomassen 2008, Muendlein 2015, Wong-Brown 2015, Dudley 2018). BRCA1 c.4986+3G>C was not observed in large population cohorts (Lek 2016). The guanine (G) nucleotide that is altered is not conserved. Based on currently available evidence, we consider BRCA1 c.4986+3G>C to be a likely pathogenic variant.
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	RCV000112443	SCV000326080	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2015-10-02	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000236214	SCV000605896	likely pathogenic	not provided	2018-06-30	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000162881	SCV000688528	likely pathogenic	Hereditary cancer-predisposing syndrome	2024-05-07	criteria provided, single submitter	clinical testing	This variant causes a G>C nucleotide substitution at the +3 position of intron 15 of the BRCA1 gene. RNA studies have observed aberrant splicing in carrier RNA that is expected to result in an absent or non-functional protein product (PMID: 23239986, 31843900). A functional study has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been detected in at least five individuals affected with breast, ovarian and pancreatic cancer (PMID: 12491499, 25682074, 25971625, 29360161, 35409996) and in suspected hereditary breast and ovarian cancer families (PMID: 18465347, 23772696). However, a multifactorial analysis has reported contradictory low segregation likelihood ratio for pathogenicity (LR) of 0.0001 and high tumor pathology LR of 418.5086 for this variant (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.
GeneKor MSA	RCV000236214	SCV000693496	likely pathogenic	not provided	2020-01-01	criteria provided, single submitter	clinical testing	This variant occurs three bases after exon 15 of the BRCA1 gene. Experimental studies have shown that this variant causes aberrant splicing in vitro, resulting in an out-of-frame insertion predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (PMID: 23239986). This variant has been observed in multiple individuals with a personal and/or family history of breast and/or ovarian cancer (PMID: 23239986, 12491499). This variant is also known as BRCA1 IVS16+3G>C and 5105G>C using alternate nomenclature. The mutation database ClinVar contains several entries for this variant (Variation ID: 55341).
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV000236214	SCV001447643	likely pathogenic	not provided	2020-10-23	criteria provided, single submitter	clinical testing
Department of Molecular Diagnostics, Institute of Oncology Ljubljana	RCV000112443	SCV001499668	likely pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2020-04-02	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000048721	SCV001774695	pathogenic	Hereditary breast ovarian cancer syndrome	2021-07-25	criteria provided, single submitter	clinical testing	Variant summary: BRCA1 c.4986+3G>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 abolishes a 5 splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Wappenschmidt_2012). The variant was absent in 249776 control chromosomes (gnomAD). c.4986+3G>C has been reported in the literature in multiple individuals affected with breast and ovarian cancers (example: Rebbeck_2018, Wappenschmidt_2012). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence suggesting a loss on protein function (Findlay_2018). 12 ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic/pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
MGZ Medical Genetics Center	RCV000112443	SCV002581629	likely pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2022-08-11	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000236214	SCV003917925	pathogenic	not provided	2023-01-01	criteria provided, single submitter	clinical testing	BRCA1: PP1:Strong, PM2, PS4:Moderate, PP3, PS3:Supporting
Baylor Genetics	RCV000112443	SCV004217009	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2024-03-05	criteria provided, single submitter	clinical testing
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	RCV000048721	SCV005045789	pathogenic	Hereditary breast ovarian cancer syndrome	2023-11-13	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV004804013	SCV005426852	pathogenic	BRCA1-related cancer predisposition	2024-04-02	criteria provided, single submitter	clinical testing	The variant c.4986+3G>C in the BRCA1 gene is located in intron 15 and is predicted to result in aberrant splicing and a disrupted or absent protein product (SpliceAI donor loss score 0.93). This variant (also known as IVS16+3G>C) has been observed in multiple individuals with breast cancer, triple negative breast cancer, ovarian cancer, pancreatic cancer, or suspected breast and ovarian cancer (PMID: 12491499, 18465347, 23239986, 23772696, 25682074, 25971625, 29360161, 29446198, 30322717). Experimental studies have shown that this variant results in retention of 65 intronic nucleotides and leads to the protein change p.Met1663Valfs*14 (PMID: 23239986). Functional studies have also shown this variant to result in loss of function with impact on haploid cell survival (PMID: 30209399). This variant is absent in the general population database, gnomAD. Truncating variants in BRCA1 gene are known to be pathogenic (PMID: 21989022, 17661172, 22762150). Therefore, this variant is classified as pathogenic.
Breast Cancer Information Core (BIC) (BRCA1)	RCV000112443	SCV000145233	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2002-05-29	no assertion criteria provided	clinical testing
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	RCV000048721	SCV000587438	likely pathogenic	Hereditary breast ovarian cancer syndrome	2015-12-17	no assertion criteria provided	research
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001353420	SCV000591552	likely pathogenic	Malignant tumor of breast		no assertion criteria provided	clinical testing	The BRCA1 c.4986+3G>C variant was identified in 3 of 1748 proband chromosomes (frequency: 0.002) from individuals or families with breast and ovarian cancer (Muendlein 2015, Wong-Brown 2015). The variant was also identified in dbSNP (ID: rs80358023) as “With Pathogenic allele”, Clinvitae database (as uncertain significance by ClinVar and Invitae, as Pathogenic by ClinVar), ARUP Laboratories BRCA Mutations Database (as definitely pathogenic), the ClinVar database (as uncertain significance by Invitae, Ambry Genetics; as likely pathogenic by GeneDx; as pathogenic by Counsyl and BIC), the BIC database (11X with clinical importance).rnThe c.4986+3G>C variant is located in the 5' splice region but does not affect the invariant +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition, 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In addition, the variant was found in triple-negative patient in preclinical study by Wong-Brown (2015). The study suggests the variant leads to intronic retention of 65 bp and creates premature stop codon at position 1663 (p.Met1663ValfsX14) and classified it as likely pathogenic. 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.
Brotman Baty Institute, University of Washington	RCV000112443	SCV001243312	not provided	Breast-ovarian cancer, familial, susceptibility to, 1		no assertion provided	in vitro
King Laboratory, University of Washington	RCV001171416	SCV001251321	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1; Hereditary breast ovarian cancer syndrome	2019-09-01	no assertion criteria provided	research
BRCAlab, Lund University	RCV000112443	SCV004243965	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2020-03-02	no assertion criteria provided	clinical testing
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne	RCV000048721	SCV005374634	likely pathogenic, low penetrance	Hereditary breast ovarian cancer syndrome	2024-10-10	no assertion criteria provided	curation	Taking into accout the results of the splice analysis and the low LRs from segregation analysis we assume that this variant is likely to be a variant with reduced penetrance in comparision with other LOF-variants in BRCA1; According to the ClinGen ENIGMA BRCA1 v1.1.0 criteria we chose these criteria: PS1 (medium pathogenic): Apply PS1_Moderate, for exonic and intronic variants with same predicted impact on splicing, as a previously classified (likely) pathogenic variant. Vary weight depending on relative positions, and confidence in classification of the reference variant. Various variants in this splice site are classified as pathogenic e.g. c.4986+6T>G; +1/2, PS3 (strong pathogenic): Findlay et al. (PS3 met as per ENIGMA/ClinGen table 9), PM2 (supporting pathogenic): not in gnomAD (90 families in GC-HBOC), PP3 (supporting pathogenic): Variant is predicted to have a splice effect by SpliceAI (threshold: 0.2, value: 0.93).