ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.1737A>G (p.Lys579=) (rs61756467)

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Total submissions: 21
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000030244 SCV000107281 likely benign Lynch syndrome 2013-09-05 reviewed by expert panel research Synonymous substitution with no effect on splicing, tested with an NMD inhibitor. Multifactorial likelihood analysis posterior probability 0.001-0.049
GeneDx RCV000194267 SCV000170344 benign not specified 2013-12-12 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000126818 SCV000212694 likely benign Hereditary cancer-predisposing syndrome 2014-06-27 criteria provided, single submitter clinical testing This alteration is classified as likely 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.
Genetic Services Laboratory, University of Chicago RCV000194267 SCV000248074 likely benign not specified 2015-07-31 criteria provided, single submitter clinical testing
Invitae RCV001079889 SCV000252654 benign Hereditary nonpolyposis colorectal neoplasms 2020-11-27 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000194267 SCV000303160 likely benign not specified criteria provided, single submitter clinical testing
Color Health, Inc RCV000126818 SCV000537405 benign Hereditary cancer-predisposing syndrome 2015-04-22 criteria provided, single submitter clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000625240 SCV000744277 likely benign Lynch syndrome I 2017-06-28 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000625240 SCV000745642 likely benign Lynch syndrome I 2015-08-07 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000679296 SCV000806010 likely benign not provided 2016-10-03 criteria provided, single submitter clinical testing
Mendelics RCV000625240 SCV001135742 likely benign Lynch syndrome I 2019-05-28 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000679296 SCV001152280 likely benign not provided 2020-03-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000194267 SCV001156596 benign not specified 2018-10-03 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000625240 SCV001299643 likely benign Lynch syndrome I 2019-05-07 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000030244 SCV000052911 benign Lynch syndrome 2015-02-17 no assertion criteria provided clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000194267 SCV000257150 likely benign not specified no assertion criteria provided research
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353525 SCV000592518 benign Carcinoma of colon no assertion criteria provided clinical testing The p.Lys579Lys variant has been identified in 5 out of 3696 proband chromosomes (frequency 0.001) in colorectal patients with Bethesda, Amsterdam or HNPCC criteria, and in 1 out of 400 control chromosomes (frequency 0.003) (Curia 1999, Scartozzi 2002, Auclair 2005, Mangold 2005, Pastrello 2011). it is listed in dbSNP database (‘with unknown allele’) (ID#: rs61756467) with an average heterozygosity of 0.002+/-0.030, therefore increasing the likelihood that this variant is benign. In addition, this variant is not expected to have clinical significance because it does not alter an amino acid residue, and is not located near a splice junction. In summary, based on the above information this variant is classified as Benign.
True Health Diagnostics RCV000126818 SCV000805267 likely benign Hereditary cancer-predisposing syndrome 2018-04-30 no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000679296 SCV001922997 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000194267 SCV001931907 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000679296 SCV001959287 likely benign not provided no assertion criteria provided clinical testing

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