ClinVar Miner

Submissions for variant NM_000238.3(KCNH2):c.558C>T (p.Gly186=) (rs139533994)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000620996 SCV000735728 likely benign Cardiovascular phenotype 2016-06-14 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Synonymous alterations with insufficient evidence to classify as benign
Athena Diagnostics Inc RCV000589337 SCV000842498 benign not provided 2018-06-20 criteria provided, single submitter clinical testing
GeneDx RCV000181718 SCV000234021 benign not specified 2013-01-14 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.
Integrated Genetics/Laboratory Corporation of America RCV000589337 SCV000696034 benign not provided 2017-03-13 criteria provided, single submitter clinical testing Variant summary: The KCNH2 c.558C>T (p.Gly186Gly) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a benign outcome for this variant. 2/5 splice prediction tools predict a creation of a cryptic splice donor site. ESE finder predicts that this variant may affect binding of ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 6/2504 control chromosomes from 1000 genomes project at a frequency of 0.0023962, which is approximately 24 times the estimated maximal expected allele frequency of a pathogenic KCNH2 variant (0.0001), suggesting this variant is likely a benign polymorphism. It was only found in African subpopulation with an allele frequency of 0.005 (6/1322 chromosomes). In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign. Taken together, this variant is classified as Benign.
Invitae RCV000206441 SCV000260585 likely benign Long QT syndrome 2018-01-10 criteria provided, single submitter clinical testing

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