ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.1886A>G (p.Gln629Arg) (rs61756468)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000076314 SCV000107335 no known pathogenicity Lynch syndrome 2013-09-05 reviewed by expert panel research Multifactorial likelihood analysis posterior probability <0.001
Invitae RCV001079970 SCV000166267 benign Hereditary nonpolyposis colorectal neoplasms 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000121562 SCV000170345 benign not specified 2014-05-05 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 RCV000129036 SCV000172946 benign Hereditary cancer-predisposing syndrome 2014-11-18 criteria provided, single submitter clinical testing In silico models in agreement (benign);Other data supporting benign classification;Other strong data supporting benign classification;Subpopulation frequency in support of benign classification
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center RCV000490519 SCV000267400 uncertain significance Lynch syndrome I 2016-03-18 criteria provided, single submitter reference population
Illumina Clinical Services Laboratory,Illumina RCV000490519 SCV000430930 likely benign Lynch syndrome I 2017-04-27 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000121562 SCV000601445 likely benign not specified 2016-10-12 criteria provided, single submitter clinical testing
Color RCV000129036 SCV000684992 benign Hereditary cancer-predisposing syndrome 2015-02-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587872 SCV000696228 benign not provided 2016-09-06 criteria provided, single submitter clinical testing Variant summary: The MSH2 c.1886A>G (p.Gln629Arg) variant involves the alteration of a non-conserved nucleotide. 3/3 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 159/123118 control chromosomes, predominantly observed in the East Asian subpopulation at a frequency of 0.0174486 (151/8654). This frequency is about 31 times the estimated maximal expected allele frequency of a pathogenic MSH2 variant (0.0005683), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. This variant has also been reported in colorectal patients or HNPCC-related cancer without strong evidence for pathogenicity. In a family, while affected proband carried the variant, another affected cousin did not carry the variant, possibly suggesting that it did not co-segregate with disease in the family (Woo_2014). Multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as Benign.
PreventionGenetics,PreventionGenetics RCV000121562 SCV000806016 benign not specified 2017-08-02 criteria provided, single submitter clinical testing
ITMI RCV000121562 SCV000085756 not provided not specified 2013-09-19 no assertion provided reference population
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000121562 SCV000691907 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam RCV000490519 SCV000745643 benign Lynch syndrome I 2017-07-04 no assertion criteria provided clinical testing

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