ClinVar Miner

Submissions for variant NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) (rs11571833)

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Total submissions: 43
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000031849 SCV000244498 benign Breast-ovarian cancer, familial 2 2016-02-16 reviewed by expert panel curation Case-control and frequency data indicate that K3326X does not confer a high risk of cancer (OR 1.3-1.5, dependent on breast or ovarian cancer subtype).
Invitae RCV000045926 SCV000073939 benign Hereditary breast and ovarian cancer syndrome 2020-12-04 criteria provided, single submitter clinical testing
Counsyl RCV000031849 SCV000154053 benign Breast-ovarian cancer, familial 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 Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;Co-occurence with mutation in same gene (phase unknown);General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance;Intact protein function observed in appropriate functional assay(s);Other strong data supporting benign classification;Seen in trans with a mutation or in homozygous state in individual without severe disease for that gene
Michigan Medical Genetics Laboratories,University of Michigan RCV000031849 SCV000196031 benign Breast-ovarian cancer, familial 2 2014-11-03 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 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 and 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 and ovarian cancer syndrome 2015-07-09 criteria provided, single submitter clinical testing
Color Health, Inc RCV000128910 SCV000292115 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000120374 SCV000301783 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000031849 SCV000383808 likely benign Breast-ovarian cancer, familial 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 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 RCV001283531 SCV000602758 benign none provided 2020-08-07 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 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 2 2015-09-21 criteria provided, single submitter clinical testing
Mendelics RCV000031849 SCV001139281 benign Breast-ovarian cancer, familial 2 2019-05-28 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000034474 SCV001149001 likely benign not provided 2018-06-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,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 uncertain significance Breast-ovarian cancer, familial 2 2017-09-21 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
Research and Development, ARUP Laboratories RCV001642529 SCV001853978 benign Breast-ovarian cancer, familial 2; Breast-ovarian cancer, familial 1; Hereditary breast and ovarian cancer syndrome 2019-07-01 criteria provided, single submitter curation
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 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 2 2002-05-29 no assertion criteria provided clinical testing
Pathway Genomics RCV000031849 SCV000187732 likely benign Breast-ovarian cancer, familial 2 2014-07-24 no assertion criteria provided literature only
GeneReviews RCV000031849 SCV000484958 pathogenic Breast-ovarian cancer, familial 2 2016-12-15 no assertion criteria 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 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
Human Genetics - Radboudumc,Radboudumc RCV000120374 SCV001952876 benign not specified no assertion criteria provided clinical testing

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