Submissions for variant NM_000059.4(BRCA2):c.9196C>T (p.Gln3066Ter) (rs80359180)

Total submissions: 17

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	RCV000077463	SCV000282469	pathogenic	Breast-ovarian cancer, familial 2	2016-04-22	reviewed by expert panel	curation	Variant allele predicted to encode a truncated non-functional protein.
Invitae	RCV000257912	SCV000073758	pathogenic	Hereditary breast and ovarian cancer syndrome	2019-12-23	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal at codon 3066 (p.Gln3066*) of the BRCA2 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individuals with breast cancer, ovarian cancer, and Fanconi anemia (PMID: 24504028, 26845104, 26681682, 24728189, 14559878, 16825431). ClinVar contains an entry for this variant (Variation ID: 9347). Loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics	RCV000131052	SCV000185982	pathogenic	Hereditary cancer-predisposing syndrome	2018-12-11	criteria provided, single submitter	clinical testing	Alterations resulting in premature truncation (e.g.reading frame shift, nonsense)
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario	RCV000257912	SCV000219421	pathogenic	Hereditary breast and ovarian cancer syndrome	2017-04-01	criteria provided, single submitter	clinical testing
University of Washington Department of Laboratory Medicine, University of Washington	RCV000210196	SCV000266051	pathogenic	Breast-ovarian cancer, familial 1	2015-11-20	criteria provided, single submitter	clinical testing
GeneDx	RCV000235644	SCV000292978	pathogenic	not provided	2018-03-07	criteria provided, single submitter	clinical testing	This pathogenic variant is denoted BRCA2 c.9196C>T at the cDNA level and p.Gln3066Ter (Q3066X) at the protein level. Using alternate nomenclature, this variant would be defined as BRCA2 9424C>T. The substitution creates a nonsense variant, which changes a Glutamine to a premature stop codon (CAG>TAG), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been identified in multiple individuals with breast or ovarian cancer, including at least one male with a personal and family history of breast cancer (Tai 2007, Fackenthal 2012, Cunningham 2014, Couch 2015, Eccles 2016). BRCA2 Gln2066Ter has also been found to co-occur with another BRCA2 pathogenic variant in at least two cases of Fanconi anemia (Offit 2003, Alter 2007). We consider this variant to be pathogenic.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000077463	SCV000296693	pathogenic	Breast-ovarian cancer, familial 2	2015-03-30	criteria provided, single submitter	clinical testing
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	RCV000077463	SCV000328076	pathogenic	Breast-ovarian cancer, familial 2	2015-10-02	criteria provided, single submitter	clinical testing
Counsyl	RCV000077463	SCV000677706	pathogenic	Breast-ovarian cancer, familial 2	2015-07-13	criteria provided, single submitter	clinical testing
Color	RCV000131052	SCV000684033	pathogenic	Hereditary cancer-predisposing syndrome	2020-01-15	criteria provided, single submitter	clinical testing
Integrated Genetics/Laboratory Corporation of America	RCV000257912	SCV000695217	pathogenic	Hereditary breast and ovarian cancer syndrome	2020-09-21	criteria provided, single submitter	clinical testing	Variant summary: BRCA2 c.9196C>T (p.Gln3066X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 251286 control chromosomes. c.9196C>T has been widely reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome and subsequently cited by others (example Rebbeck_2018, a comprehensive collection of reported cases identified in the CIMBA database). These data indicate that the variant is very likely to be associated with disease. Eleven clinical diagnostic laboratories and one expert panel (ENIGMA) have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories	RCV000235644	SCV000885103	pathogenic	not provided	2018-06-14	criteria provided, single submitter	clinical testing	The BRCA2 c.9196C>T; p.Gln3066Ter variant (rs80359180), also known as c.9424C>T, has been described in individuals with breast cancer, ovarian cancer, and Fanconi anemia (Alter 2007, Cunningham 2014, Fackenthal 2012, Offit 2003, Song 2014). It is reported as pathogenic by several laboratories in ClinVar (Variation ID: 9347) and is absent from general population databases (1000 Genomes Project, Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. This variant induces an early termination codon and is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered pathogenic. References: Alter B et al. Clinical and molecular features associated with biallelic mutations in FANCD1/BRCA2. J Med Genet. 2007 Jan;44(1):1-9. Cunningham J et al. Clinical characteristics of ovarian cancer classified by BRCA1, BRCA2, and RAD51C status. Sci Rep. 2014 Feb 7;4:4026. Fackenthal J et al. High prevalence of BRCA1 and BRCA2 mutations in unselected Nigerian breast cancer patients. Int J Cancer. 2012 Sep 1;131(5):1114-23. Offit K et al. Shared genetic susceptibility to breast cancer, brain tumors, and Fanconi anemia. J Natl Cancer Inst. 2003 Oct 15;95(20):1548-51. Song H et al. The contribution of deleterious germline mutations in BRCA1, BRCA2 and the mismatch repair genes to ovarian cancer in the population. Hum Mol Genet. 2014 Sep 1;23(17):4703-9.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine	RCV000257912	SCV000967781	pathogenic	Hereditary breast and ovarian cancer syndrome	2018-05-08	criteria provided, single submitter	clinical testing	The p.Gln3066X variant in BRCA2 has been reported >10 individuals with BRCA2-ass ociated cancers and in 2 individuals with Fanconi anemia have had a second BRCA2 pathogenic variant (Offit 2003, Alter 2007, Tai 2007, Fackenthal 2012, Cunningh am 2014, Song 2014, Couch 2015, Eccles 2016, Breast Cancer Information Core (BIC )). It was also absent from large population studies. This nonsense variant lead s to a premature termination codon at position 3066, which is predicted to lead to a truncated or absent protein. Heterozygous loss of function of the BRCA2 gen e is an established disease mechanism in hereditary breast and ovarian cancer (H BOC). In addition, this variant was classified as Pathogenic by the ClinGen-appr oved ENIGMA expert panel (ClinVar SCV000282469.1). In summary, this variant meet s criteria to be classified as pathogenic for HBOC in an autosomal dominant mann er. ACMG/Amp Criteria Applied: PVS1, PS4, PM2.
OMIM	RCV000009941	SCV000030162	pathogenic	Fanconi anemia, complementation group D1	2007-01-01	no assertion criteria provided	literature only
Sharing Clinical Reports Project (SCRP)	RCV000077463	SCV000109261	pathogenic	Breast-ovarian cancer, familial 2	2012-10-26	no assertion criteria provided	clinical testing
Breast Cancer Information Core (BIC) (BRCA2)	RCV000077463	SCV000147566	pathogenic	Breast-ovarian cancer, familial 2	2002-05-29	no assertion criteria provided	clinical testing
Research Molecular Genetics Laboratory,Women's College Hospital, University of Toronto	RCV000257912	SCV000587991	pathogenic	Hereditary breast and ovarian cancer syndrome	2014-01-31	no assertion criteria provided	research