ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.1680T>C (p.Asn560=) (rs200056411)

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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 RCV000126817 SCV000212795 likely benign Hereditary cancer-predisposing syndrome 2014-07-07 criteria provided, single submitter clinical testing
Color RCV000126817 SCV000684966 benign Hereditary cancer-predisposing syndrome 2015-07-22 criteria provided, single submitter clinical testing
GeneDx RCV000212605 SCV000170343 benign not specified 2013-12-18 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.
Illumina Clinical Services Laboratory,Illumina RCV000076241 SCV000430929 uncertain significance Lynch syndrome 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587483 SCV000696222 benign not provided 2016-06-27 criteria provided, single submitter clinical testing Variant summary: The MSH2 c.1680T>C (p.Asn560Asn) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splicing algorithms predict no change to normal splicing, and ex vivo splicing assay showed this variant does not affect splicing. This variant was found in 42/120644 control chromosomes, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0006173 (41/66422). This frequency is greater than 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 European (Non-Finnish) origin. In addition, the variant was found to co-occur with a pathogenic MSH2 variant, c.1079T>A (p.Leu360X), in one individual reported by UMD. Furthermore, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as Benign.
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000076241 SCV000107260 likely benign Lynch syndrome 2013-09-05 reviewed by expert panel research Synonymous substitution with no effec on splicing, tested with NMD inhibitor
Invitae RCV000524353 SCV000253152 benign Hereditary nonpolyposis colon cancer 2017-12-27 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000212605 SCV000601435 benign not specified 2017-06-07 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587483 SCV000889422 benign not provided 2017-06-07 criteria provided, single submitter clinical testing

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