ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.471C>A (p.Gly157=) (rs61756463)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000126822 SCV000212810 likely benign Hereditary cancer-predisposing syndrome 2014-07-16 criteria provided, single submitter clinical testing
CSER_CC_NCGL; University of Washington Medical Center RCV000076604 SCV000212176 likely benign Lynch syndrome 2015-03-11 criteria provided, single submitter research
Color RCV000126822 SCV000685094 benign Hereditary cancer-predisposing syndrome 2015-11-30 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000625237 SCV000744268 likely benign Lynch syndrome I 2017-06-28 criteria provided, single submitter clinical testing
GeneDx RCV000212586 SCV000170348 benign not specified 2014-04-08 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.
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam RCV000625237 SCV000745633 benign Lynch syndrome I 2016-07-20 no assertion criteria provided clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586050 SCV000696270 benign not provided 2016-06-20 criteria provided, single submitter clinical testing Variant summary: The MSH2 c.471C>A (p.Gly157Gly) 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. This variant was found in 132/121410 control chromosomes, predominantly observed in the East Asian subpopulation at a frequency of 0.0146753 (127/8654). This frequency is about 26 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 been reported in multiple affected individuals and all are East Asians. The studies reporting this variant mostly detected variant in controls with higher or comparable MAF as in case cohorts. In addition, variant was detected to co-occur with a likely disease variant (c.-80insA) that can explain the disease phenotype, further supporting the benign classification of this variant. 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) RCV000076604 SCV000107640 likely benign Lynch syndrome 2013-09-05 reviewed by expert panel research Synonymous substitution with no effect on splicing & MAF 0.01-1%
Invitae RCV000524410 SCV000252656 benign Hereditary nonpolyposis colon cancer 2018-01-12 criteria provided, single submitter clinical testing
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000212586 SCV000691897 benign not specified no assertion criteria provided clinical testing
PreventionGenetics RCV000212586 SCV000806043 benign not specified 2017-06-12 criteria provided, single submitter clinical testing

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