Submissions for variant NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter)

gnomAD frequency: 0.00597  dbSNP: rs11571833

Total submissions: 48

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen	RCV000031849	SCV004101446	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2023-10-12	reviewed by expert panel	curation	The c.9976A>T variant in BRCA2 is predicted to cause a change in the length of the protein due to the insertion of a terminating codon instead of the usual Lysine at amino acid 3326 (p.Lys3326Ter). The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth >=20) or gnomAD v3.1 (non-cancer subset, read depth >=20) is 0.00813 in the European (non-Finnish) population, which is above the ENIGMA BRCA1/2 VCEP threshold (>0.001) for BA1 (BA1 met). Nonsense variant predicted to cause a premature stop codon that is predicted to escape nonsense mediated decay, and lead to truncation of a region with unknown protein function (sequence up to BRCA2:p.Glu3309 is maintained) (PVS1 not met). Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID: 29988080) (BS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 3.09E-263 (based on Cosegregation LR=0.001; Pathology LR=1.864E-35; Co-occurrence LR=0.0001; Case-Control LR=1.66E-221), below the threshold for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; PMID: 18451181). In summary, this variant meets the criteria to be classified as a Benign variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BA1, BS3, BP5_Very strong).
Invitae	RCV000045926	SCV000073939	benign	Hereditary breast ovarian cancer syndrome	2024-02-01	criteria provided, single submitter	clinical testing
Counsyl	RCV000031849	SCV000154053	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2014-01-02	criteria provided, single submitter	literature only
Ambry Genetics	RCV000128910	SCV000172777	benign	Hereditary cancer-predisposing syndrome	2014-11-19	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Michigan Medical Genetics Laboratories, University of Michigan	RCV000031849	SCV000196031	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2014-11-03	criteria provided, single submitter	clinical testing
Eurofins Ntd Llc (ga)	RCV000120374	SCV000202309	benign	not specified	2015-10-13	criteria provided, single submitter	clinical testing
CSER _CC_NCGL, University of Washington	RCV000045926	SCV000212199	benign	Hereditary breast ovarian cancer syndrome	2015-03-11	criteria provided, single submitter	research
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV000735635	SCV000219429	likely benign	Breast and/or ovarian cancer	2017-12-19	criteria provided, single submitter	clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	RCV000045926	SCV000257622	benign	Hereditary breast ovarian cancer syndrome	2015-07-09	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000128910	SCV000292115	benign	Hereditary cancer-predisposing syndrome	2014-11-19	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000120374	SCV000301783	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000031849	SCV000383808	likely benign	Breast-ovarian cancer, familial, susceptibility to, 2	2018-03-06	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV000034474	SCV000511377	benign	not provided	2016-12-27	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV000031849	SCV000575759	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2016-02-22	criteria provided, single submitter	clinical testing
Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency	RCV000120374	SCV000586993	benign	not specified	2017-04-18	criteria provided, single submitter	clinical testing
Department of Pathology and Molecular Medicine, Queen's University	RCV000120374	SCV000588130	benign	not specified	2017-04-20	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000034474	SCV000602758	benign	not provided	2023-11-22	criteria provided, single submitter	clinical testing
GeneKor MSA	RCV000120374	SCV000693648	benign	not specified	2017-11-01	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000034474	SCV000695284	benign	not provided	2016-08-12	criteria provided, single submitter	clinical testing	Variant summary: The BRCA2 c.9976A>T (p.Lys3326X) variant results in a termination codon at the penultimate exon, predicted to cause a truncation of the last 93 amino acids. This variant is not expected to affect any known domain (InterPro) and no truncations downstream of this position have been reported to be pathogenic in literature and databases. This variant was found in 2327/296226 control chromosomes (including 8 homozygotes) at a frequency of 0.0078555, which is approximately 10 times the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this variant is likely a benign polymorphism. In addition, several clinical diagnostic laboratories/reputable databases have classified this variant as benign (14)/likely benign (1). Available family, co-occurrence and functional data also show that it is not a disease causing variant. Despite these, this variant is found at considerably high frequency, especially in patients with breast and/or ovarian cancer, raising a possibilty that it may be a risk variant. Using weighted logistic regression, Meeks et al 2016 analyzed data from the large iCOGS study including 76637 cancer case patients and 83796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Other adjustments in the study were adjustment for attained age, consortium study site, and principal components of population structure. From the study, weighted ORs for invasive breast cancer and ovarian cancers were 1.28 (confidence interval 1.17-1.4; P-value=3.84x10e-3) and 1.26 (confidence interval 1.1-1.43; P-value=3.84x10e-3), respectively. The authors conclude that this study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Hence this variant is a risk allele which attributes a significant but a low risk in development of breast or ovarian cancer. In addition, other genetic/lifestyle/environmental factors may also be playing a part in elevation of risk. Taken together, this variant is classified as Benign for HBOC.
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000031849	SCV000743529	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2014-10-09	criteria provided, single submitter	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000031849	SCV000744794	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2015-09-21	criteria provided, single submitter	clinical testing
Mendelics	RCV000031849	SCV001139281	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2019-05-28	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000034474	SCV001149001	likely benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing	BRCA2: BS2
Illumina Laboratory Services, Illumina	RCV001112896	SCV001270610	likely benign	Fanconi anemia complementation group D1	2018-03-06	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Institute of Human Genetics, University of Leipzig Medical Center	RCV000031849	SCV001429528	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2021-10-06	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000120374	SCV001469470	benign	not specified	2020-05-11	criteria provided, single submitter	clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000034474	SCV002010281	benign	not provided	2021-11-03	criteria provided, single submitter	clinical testing
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State	RCV000045926	SCV002025886	uncertain significance	Hereditary breast ovarian cancer syndrome	2022-04-19	criteria provided, single submitter	clinical testing
Genetics Program, Instituto Nacional de Cancer	RCV000045926	SCV002515170	benign	Hereditary breast ovarian cancer syndrome	2021-11-01	criteria provided, single submitter	research
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000120374	SCV002551855	benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Genetics and Molecular Pathology, SA Pathology	RCV000031849	SCV002556659	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2022-06-02	criteria provided, single submitter	clinical testing	The BRCA2 c.9976A>T variant is classified as Benign (BS2)
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV000031849	SCV004016857	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2023-07-07	criteria provided, single submitter	clinical testing
Biesecker Lab/Clinical Genomics Section, National Institutes of Health	RCV000034474	SCV000043239	no known pathogenicity	not provided	2012-07-13	no assertion criteria provided	research	Converted during submission to Benign.
Sharing Clinical Reports Project (SCRP)	RCV000031849	SCV000054457	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2012-05-01	no assertion criteria provided	clinical testing
ITMI	RCV000120374	SCV000084526	not provided	not specified	2013-09-19	no assertion provided	reference population
Breast Cancer Information Core (BIC) (BRCA2)	RCV000031849	SCV000145737	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2002-05-29	no assertion criteria provided	clinical testing
Pathway Genomics	RCV000031849	SCV000187732	likely benign	Breast-ovarian cancer, familial, susceptibility to, 2	2014-07-24	no assertion criteria provided	literature only
GeneReviews	RCV000031849	SCV000484958	not provided	Breast-ovarian cancer, familial, susceptibility to, 2		no assertion provided	literature only
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	RCV000120374	SCV000588018	benign	not specified	2014-01-31	no assertion criteria provided	research
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001004846	SCV000592309	likely benign	Malignant tumor of breast		no assertion criteria provided	clinical testing	The BRCA2 p.Lys3326X variant was identified in 1577 of 158144 proband chromosomes (frequency: 0.010) from various ethnicities in multinational cohorts of individuals or families with breast and ovarian cancer and was present in 1414 of 167882 control chromosomes (frequency: 0.008) from healthy individuals (Hadjisavvas 2004 15172753, Wagner 1999 9971877, Borg 2010 20104584, Claes 2003 12759930, Meeks 2016 26586665). The variant was also identified in dbSNP (ID: rs11571833) as “With other allele”, ClinVar (Benign by ENIGMA, DVD CHOP, Michigan Medical Genetics, CSER_CC_NCGL University of Washington Medical Center, Colour Genomics, Prevention Genetics, Invitae, Counsyl, Ambry Genetics, Laboatroy Corporation of America Study Description, Children's Mercy Hospital, Fulgent, Cancer Genetic and Genomic Laboratory BC, EGL Genetic Diagnostics, Queen's University Department of Pathology, ARUP, Women's College Hospital, BIC, SCRP, and Biesecker Lab, as likely benign by Illumina, CHEO, and Pathway Genomics and as pathogenic by GeneReviews.), in ClinVitae (7x as Benign in 4 entries including 3 from ClinVar and 1 from EmyClass, as Conflicting interpretations of pathogenicity from Invitae and ClinVar, and as a polymorphism by kConFab), COSMIC (1x observed in alveolar rhabdomyosarcoma, as neutral), LOVD 3.0 (65x as does not affect function, affect unknown or unclassified), UMD-LSDB (114 entries, classified as neutral and reported as co-occuring with pathogenic BRCA2 and BRCA1 variants), BIC Database (301 entries, classification pending), and ARUP Laboratories (classified as not pathogenic or of no clinical significance). The variant was not identified in MutDB, or the Zhejiang Colon Cancer Database. The variant was also identified by our laboratory in 111 individuals with breast, ovarian, pancreatic, or brain cancer. The variant was identified in control databases in 1782 of 276718 chromosomes (13 homozygous) at a frequency of 0.006 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include African in 35 of 23984 chromosomes (freq: 0.001), Other in 48 of 6448 chromosomes (freq: 0.007), Latino in 95 of 34342 chromosomes (freq: 0.003), European Non-Finnish in 1089 of 126410 chromosomes (freq: 0.009), Ashkenazi Jewish in 41 of 10146 chromosomes (freq: 0.004), European Finnish in 266 of 25780 chromosomes (freq: 0.01), and South Asian in 208 of 30764 chromosomes (freq: 0.007) while the variant was not observed in the East Asian population. The c.9976A>T variant leads to a premature stop codon in the penultimate exon of BRCA2 and is predicted to cause a truncation of the last 93 amino acids. There is conflicting evidence in the literature regarding the significance of this variant. The variant was shown to have a 1.26 fold increase in breast cancer risk (in heterozygous form) or 5.78 increase risk (in homozygous form) (95% confidence interval p=1.2x10-5) and/or is in linkage disequilibrium with higher risk variants in a study looking at SNPs selected on the basis of genome wide association studies, genotyped in 45,290 cases and 41,880 controls from 41 studies (Michailidou 2013 23535729). A more recent study of the c.9976A>T variant identified 852/41081 carriers of the variant in women with breast cancer, and 322/14514 with ovarian cancer. They determined an odds ratio of adjusted for the probability of carrying a pathogenic BRCA1/2 variant of 1.28 for the breast cancer group, 1.52 for the triple negative breast cancer group and 1.46 for the serous ovarian cancer group (Meeks 2016 26586665). A posterior probability model integrating causality models based on prior probability derived from evolutionary conservation and likelihoods of causality, indicate that this variant is not pathogenic (Lindor_2012_21990134). However, in vitro splicing assays on 31 BRCA2 variants showed this variant to be pathogenic despite not being pathogenic based on the posterior probability model (de Garibay_2013_24123850). Claes (2003 12759930) also found that 3 families carried the pathogenic 6503_6504delTT in addition to IVS24-16T>C and p.Lys3326X variants, such that the p.Lys3326X variant was in linkage disequilibrium with a true pathogenic mutation, this is also well documented on the UMD LSBD website and in additional studies (Meeks 2016_26586665, Mazoyer_1996_8896551, personal communication Myriad genetics). Case control studies have shown increased risk (1.30 to 5.00-fold) for oesophageal, pancreatic, lung and second primary breast cancers, however the clinical significance of these associations require confirmation or replication in additional studies (Martin_2005_15806175, Rudd_2006_16741161, Akbari_2011_21279724, Johnson_2007_17341484). Other conflicting evidence was seen in a study where this variant did not co-segregate with disease in a breast cancer family (Mazoyer_1996_8896551). However, homozygous or compound heterozygous variants in the BRCA2 gene have been reported to cause Fanconi anemia, and a cell line derived from one such patient carried the 10204A>T (c.9976A>T) variant and the 3033delAAAC deletion (Howlet_2002_12065746), increasing the likelihood that the p.Lys3326X variant may have clinical significance; other in vitro studies do not show any impact on BRCA2 function for the p.Lys3326X allele (Kuznetsov 2008 18607349, Farrugia 2008 18451181, Wu 2005 15695382). Despite the conflicting reports in the literature, the population data and the finding that no truncations downstream of this position have been reported to be pathogenic in the literature or databases (Laboratory Corporation of America, assessment August, 2016) strongly support a benign role for this variant. In summary, based on the above information this variant meets our laboratory's criteria to be classified as likely benign.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000031849	SCV000733342	benign	Breast-ovarian cancer, familial, susceptibility to, 2		no assertion criteria provided	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000034474	SCV000778727	likely benign	not provided	2017-02-02	no assertion criteria provided	clinical testing
True Health Diagnostics	RCV000128910	SCV000787962	benign	Hereditary cancer-predisposing syndrome	2018-02-20	no assertion criteria provided	clinical testing
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research	RCV000735635	SCV000863773	likely benign	Breast and/or ovarian cancer	2013-08-02	no assertion criteria provided	clinical testing
Center of Medical Genetics and Primary Health Care	RCV001004846	SCV000987251	benign	Malignant tumor of breast	2020-04-08	no assertion criteria provided	research	ACMG Guidelines 2015 criteria
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000034474	SCV001800500	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	RCV000120374	SCV001906363	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000120374	SCV001952876	benign	not specified		no assertion criteria provided	clinical testing