Submissions for variant NM_007294.4(BRCA1):c.4484G>T (p.Arg1495Met)

dbSNP: rs80357389

Total submissions: 24

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000048576	SCV000076589	pathogenic	Hereditary breast ovarian cancer syndrome	2024-01-11	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with methionine, which is neutral and non-polar, at codon 1495 of the BRCA1 protein (p.Arg1495Met). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs80357389, gnomAD 0.0009%). This missense change has been observed in individual(s) with breast and ovarian cancer (PMID: 10571952, 10923033, 22144684, 23096355, 24607278). It has also been observed to segregate with disease in related individuals. This variant is also known as 4603G>T and c.4547G>T. ClinVar contains an entry for this variant (Variation ID: 37598). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 13 and introduces a premature termination codon (PMID: 10571952, 12915465, 21120943, 24607278; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics	RCV000131886	SCV000186941	pathogenic	Hereditary cancer-predisposing syndrome	2021-09-27	criteria provided, single submitter	clinical testing	The c.4484G>T pathogenic mutation (also known as p.R1495M), located in coding exon 12 of the BRCA1 gene, results from a G to T substitution at nucleotide position 4484. The amino acid change results in arginine to methionine at codon 1495, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 12, which makes it likely to have some effect on normal mRNA splicing. The c.4484G>T mutation has been reported in hereditary breast and ovarian cancer patients and multiple, independent splicing studies have demonstrated that it leads to exon skipping and predicted premature protein truncation (Ambry internal data; Ozcelik H et al. Hum Mutat, 1999;14:540-1; Aziz S et al. Gynecol. Oncol. 2001 Mar;80:341-5; Yang Y et al. Hum. Mol. Genet. 2003 Sep;12:2121-31; Tommasi S et al. Mutat. Res. 2008 Sep;644:64-70; Caux-Moncoutier V et al. Hum. Mutat. 2011 Mar;32:325-34; Lu W et al. Fam Cancer, 2012 Sep;11:381-5; Houdayer C et al. Hum. Mutat. 2012 Aug;33:1228-38; Lara K et al. Biol. Res. 2012;45:117-30; Ripamonti CB et al. BMC Cancer, 2013 Feb;13:46; Dodova RI et al. BMC Cancer, 2015 Jul;15:523; Maistro S et al. BMC Cancer. 2016 Dec;16:934; Palmero EI et al. Sci Rep, 2018 06;8:9188; Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620; Marchetti C et al. Ann Surg Oncol, 2018 Nov;25:3701-3708; de Souza Timoteo AR et al. Breast Cancer Res Treat, 2018 Dec;172:637-646; Cotrim DP et al. BMC Cancer, 2019 Jan;19:4; Lerner-Ellis J et al. J Cancer Res Clin Oncol, 2021 Mar;147:871-879; Artioli G et al. Gynecol Oncol, 2021 Jun;161:755-761). This mutation was also reported in a patient with endometrial cancer who also had family history of ovarian cancer (Vietri MT et al. Med Oncol, 2021 Jan;38:13). In addition, this alteration has been classified as pathogenic (p>0.99) by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, and mutation co-occurrence (Easton DF et al. Am. J. Hum. Genet. 2007 Nov;81:873-83; Lindor NM et al. Hum. Mutat. 2012 Jan;33:8-21; Vallee MP et al. Hum. Mutat. 2012 Jan;33:22-8). Of note, this alteration is also designated as 4603G>T in published literature. This nucleotide position is highly conserved in available vertebrate species. In addition, In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the available evidence, this alteration is classified as a pathogenic mutation.
GeneDx	RCV000159992	SCV000210177	pathogenic	not provided	2022-01-04	criteria provided, single submitter	clinical testing	Published splicing studies demonstrate a damaging effect: Exonic splice resulting in out-of-frame skipping of exon 13, as well as minor amounts of transcript with in-frame skipping of exons 13-14 (also referred to as exons 14 and 15 in the literature) (Ozcelik 1999, Yang 2003, Houdayer 2012, Colombo 2013, Santos 2014); Observed in multiple individuals with personal and/or family histories of breast and ovarian cancer, segregating with cancer in at least one of these families (Aziz 2001, Caux-Moncoutier 2011, Zhang 2011, Lara 2012, Ripamonti 2013, Santos 2014, Pal 2015, Finch 2015, Pellegrino 2016, Brianese 2017); Multifactorial studies suggest this variant is associated with breast and ovarian cancer (Lindor 2012); Not observed at significant frequency in large population cohorts (gnomAD); Also known as 4603G>T; This variant is associated with the following publications: (PMID: 25782689, 21324516, 27163896, 12915465, 26219728, 10571952, 21447777, 26913838, 23374397, 24607278, 26287763, 21120943, 25896959, 24916970, 18092194, 23096355, 17924331, 27914478, 27225819, 29116469, 28465148, 28475402, 28781887, 30283497, 29907814, 28423363, 31013702, 30606148, 30765603, 30159786, 22505045, 32885271, 29446198, 11263928, 33087888, 23451180, 32427313, 30787465, 21990134, 15343273, 22737296)
Pathway Genomics	RCV000031179	SCV000223754	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2014-10-30	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000159992	SCV000296380	pathogenic	not provided	2019-12-09	criteria provided, single submitter	clinical testing	In the published literature, it has been reported in women affected with breast cancer (PMIDs: 18694767 (2008), 26287763 (2015)), ovarian cancer (PMIDs: 10571952 (1999), 27914478 (2016)), and fallopian tube cancer (PMID: 11263928 (2001)). Functional studies have shown that this variant causes skipping of BRCA1 exon 14 (PMIDs: 12915465 (2003), 22505045 (2012), 12915465 (2003)). Based on the available information, this variant is classified as pathogenic.
GeneKor MSA	RCV000238601	SCV000296803	pathogenic	not specified	2016-07-01	criteria provided, single submitter	clinical testing
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	RCV000031179	SCV000325979	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2015-10-02	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000131886	SCV000537652	pathogenic	Hereditary cancer-predisposing syndrome	2023-03-30	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with methionine at codon 1495 and causes a G>T nucleotide substitution at the last nucleotide of exon 13 of the BRCA1 gene. Multiple RNA studies on carrier RNA and minigene splicing assay have consistently found that this variant causes the out-of-frame skipping of exon 13 resulting in a premature termination codon (PMID: 10571952, 12915465, 21120943, 22505045, 23451180, 24607278, 31843900). This variant has been reported in multiple individuals and families affected with breast and ovarian cancer (PMID: 10571952, 18092194, 18159056, 18694767, 21120943, 21324516, 22476429, 23096355, 23374397, 24607278, 27914478, 28423363, 31843900). This variant has been reported with family history and co-segregation likelihood ratios for pathogenicity of 5.28 and 2.42, respectively (PMID: 17924331, 24607278). This variant has been identified in 1/251172 chromosomes 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 Pathogenic.
Baylor Genetics	RCV000462940	SCV000540946	pathogenic	Familial cancer of breast	2017-02-23	criteria provided, single submitter	clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000048576	SCV000605750	pathogenic	Hereditary breast ovarian cancer syndrome	2020-04-14	criteria provided, single submitter	clinical testing	proposed classification - variant undergoing re-assessment, contact laboratory
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000048576	SCV000699152	pathogenic	Hereditary breast ovarian cancer syndrome	2016-07-31	criteria provided, single submitter	clinical testing	Variant summary: The BRCA1 c.4484G>T (p.Arg1495Met) variant causes a missense change involving a conserved nucleotide, located at the most 3' position, i.e., the last nucleotide of exon 13. It is predicted to disrupt the natural splice donor site and cause abnormal splicing. 5/5 splicing prediction tools, predict alterations to splicing, consistent with the observed functional studies that implicate an affect on splicing. The variant of interest was observed in a large, broad control population, ExAC, with an allele frequency of 1/121358, which does not exceed the estimated maximal expected allele frequency for a pathogenic BRCA1 variant of 1/1000. The variant of interest has been reported in multiple affected individuals via publications, along with multiple reputable databases/clinical laboratories citing the variant as "pathogenic." Therefore, taking all available lines of evidence into consideration, the variant of interest has been classified as Pathogenic.
Mendelics	RCV000048576	SCV000839231	pathogenic	Hereditary breast ovarian cancer syndrome	2018-07-02	criteria provided, single submitter	clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV000770739	SCV000902222	pathogenic	Breast and/or ovarian cancer	2022-06-28	criteria provided, single submitter	clinical testing
Mendelics	RCV000031179	SCV001140523	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2019-05-28	criteria provided, single submitter	clinical testing
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	RCV000031179	SCV002512513	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2021-07-17	criteria provided, single submitter	clinical testing	ACMG classification criteria: PS3 strong, PS3, PS4 strong, PS4, PM2 moderate, PM2, PP1 moderate, PP3 supporting
Genetics Program, Instituto Nacional de Cancer	RCV000048576	SCV002515213	pathogenic	Hereditary breast ovarian cancer syndrome	2021-11-01	criteria provided, single submitter	research
Sema4, Sema4	RCV000131886	SCV002537753	pathogenic	Hereditary cancer-predisposing syndrome	2021-11-01	criteria provided, single submitter	curation
Baylor Genetics	RCV000031179	SCV004215024	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2023-08-15	criteria provided, single submitter	clinical testing
Sharing Clinical Reports Project (SCRP)	RCV000031179	SCV000053779	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2012-05-01	no assertion criteria provided	clinical testing
Breast Cancer Information Core (BIC) (BRCA1)	RCV000031179	SCV000145100	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	RCV000048576	SCV000587401	pathogenic	Hereditary breast ovarian cancer syndrome	2014-01-31	no assertion criteria provided	research
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000159992	SCV000591519	pathogenic	not provided		no assertion criteria provided	clinical testing	The BRCA1 p.Arg1495Met variant was identified in 7 of 8214 proband chromosomes (frequency: 0.0009) from individuals or families with breast and/or ovarian cancer or fallopian tube cancer (Zhang 2011, Shattuck-Eidens 1997, Nedelcu 2002, Aziz 2001, John 2007, Pilato 2010). The variant was also identified in the following databases: dbSNP (ID: rs80357389) as “With Pathogenic allele”, ClinVar and Clinvitae (12x - classified as pathogenic by Ambry Genetics, GeneDx, Pathway Genomics, Quest Diagnostics, GeneKor, Univ. of Cambridge, Color Genomics, Baylor Miraca Genetics, Invitae, BIC, SCRP, COGR), COGR (2x - classified as pathogenic by Sinai Health System and COGR consensus), LOVD 3.0 (3x classified as affects function), UMD-LSDB (12x classified as causal), BIC Database (27 submissions, classification pending), and the ARUP Laboratories (classified as definitely pathogenic). The variant was not identified in COSMIC, MutDB, or Zhejiang Colon Cancer databases. The variant was also identified by our laboratory in 1 individual with breast cancer. The variant was identified in control databases in 1 of 245958 chromosomes at a frequency of 0.000004 (one individual of European non-Finnish ethnicity; freq. 0.000009) (Genome Aggregation Consortium Feb 27, 2017). This variant was observed by RT-PCR to result increased levels of alternative transcripts demonstrating both an out-of-frame deletion of exon 14 as well as an in-frame deletion of exons 14 and 15 (Santos 2014). Together with co-segregation data the authors conclude that this variant is considered pathogenic. A humanized mouse model system demonstrated that this variant causes aberrant splicing resulting in the deletion of exon 14 due to possible disruption of cis-acting splicing regulatory elements (Yang 2003). The p.Arg1495Met residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The p.Arg1495Met variant occurs in the last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.
King Laboratory, University of Washington	RCV001171414	SCV001251319	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1; Hereditary breast ovarian cancer syndrome	2019-09-01	no assertion criteria provided	research
BRCAlab, Lund University	RCV000031179	SCV002588812	pathogenic	Breast-ovarian cancer, familial, susceptibility to, 1	2022-08-26	no assertion criteria provided	clinical testing