ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.1255C>A (p.Gln419Lys) (rs63750006)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000160643 SCV000213572 likely benign Hereditary cancer-predisposing syndrome 2017-10-30 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: In silico models in agreement (benign),Subpopulation frequency in support of benign classification
Color RCV000160643 SCV000537420 likely benign Hereditary cancer-predisposing syndrome 2015-04-14 criteria provided, single submitter clinical testing
GeneDx RCV000121568 SCV000211245 likely benign not specified 2017-09-27 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.
ITMI RCV000121568 SCV000085764 not provided not specified 2013-09-19 no assertion provided reference population
Integrated Genetics/Laboratory Corporation of America RCV000121568 SCV000917686 likely benign not specified 2017-11-20 criteria provided, single submitter clinical testing Variant summary: The MSH2 c.1255C>A (p.Gln419Lys) variant involves the alteration of a non-conserved nucleotide. 4/4 in silico tools predict a benign outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 152/277880 control chromosomes, predominantly observed in the East Asian subpopulation at a frequency of 0.007792 (147/18866). This frequency is about 14 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. The variant has been reported in affected individuals in the literature, without strong evidence for causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign/benign, including one report of the variant being present in a patient who carries a pathogenic variant. Taken together, this variant is classified as likely benign.
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000076079 SCV000107094 likely benign Lynch syndrome 2013-09-05 reviewed by expert panel research Multifactorial likelihood analysis posterior probability 0.001-0.049
Invitae RCV000524337 SCV000260558 benign Hereditary nonpolyposis colon cancer 2018-01-02 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000121568 SCV000601426 likely benign not specified 2016-10-06 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759096 SCV000888201 benign not provided 2017-12-20 criteria provided, single submitter clinical testing

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