ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.2400A>G (p.Leu800=) (rs201298777)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000160651 SCV000212862 likely benign Hereditary cancer-predisposing syndrome 2014-06-03 criteria provided, single submitter clinical testing
Color RCV000160651 SCV000690070 likely benign Hereditary cancer-predisposing syndrome 2015-07-27 criteria provided, single submitter clinical testing
Counsyl RCV000410686 SCV000489650 likely benign Lynch syndrome I 2016-10-31 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000410686 SCV000744281 likely benign Lynch syndrome I 2017-06-28 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000724817 SCV000226006 uncertain significance not provided 2015-05-27 criteria provided, single submitter clinical testing
GeneDx RCV000212619 SCV000211253 benign not specified 2014-08-25 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 RCV000076467 SCV000430935 uncertain significance Lynch syndrome 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000212619 SCV000919695 uncertain significance not specified 2017-10-26 criteria provided, single submitter clinical testing Variant summary: The MSH2 c.2400A>G (p.Leu800Leu) 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 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE site of SRp40 and SRp55. However, these predictions have yet to be confirmed by functional studies. This variant was found in 14/277180 control chromosomes, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.000111 (14/126676), nonetheless this frequency is smaller than the estimated maximal expected allele frequency of a pathogenic MSH2 variant (0.0005683). The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign/VUS. Taken together, this variant is classified as VUS-possibly benign.
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000076467 SCV000107496 uncertain significance Lynch syndrome 2013-09-05 reviewed by expert panel research Insufficient evidence
Invitae RCV000524386 SCV000253155 likely benign Hereditary nonpolyposis colon cancer 2017-12-17 criteria provided, single submitter clinical testing

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