ClinVar Miner

Submissions for variant NM_000218.3(KCNQ1):c.-5T>C (rs532941548)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000155746 SCV000169951 benign not specified 2012-03-27 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.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000155746 SCV000205456 likely benign not specified 2018-02-28 criteria provided, single submitter clinical testing c.-5T>C in the 5'UTR of KCNQ1: This variant is classified as likely benign becau se it has been identified in 0.34% (47/13662) of European chromosomes by the Gen ome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs532 941548). ACMG/AMP Criteria applied: BS1.
Ambry Genetics RCV000242002 SCV000319135 likely benign Cardiovascular phenotype 2018-05-21 criteria provided, single submitter clinical testing Insufficient or conflicting evidence;Other data supporting benign classification;Subpopulation frequency in support of benign classification
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000725213 SCV000335034 uncertain significance not provided 2015-09-21 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000389967 SCV000370195 likely benign Long QT syndrome 1 2018-08-15 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000310463 SCV000370196 uncertain significance Atrial fibrillation, familial, 3 2018-08-15 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Clinical Services Laboratory,Illumina RCV000364999 SCV000370197 likely benign Romano-Ward syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000270523 SCV000370198 uncertain significance Short QT syndrome 2 2018-08-16 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Clinical Services Laboratory,Illumina RCV000307327 SCV000370199 uncertain significance Jervell and Lange-Nielsen syndrome 1 2018-08-15 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Athena Diagnostics Inc RCV000725213 SCV001144353 uncertain significance not provided 2018-11-19 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000725213 SCV001248097 likely benign not provided 2020-03-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000155746 SCV001339051 uncertain significance not specified 2020-03-16 criteria provided, single submitter clinical testing Variant summary: KCNQ1 c.-5T>C is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.0016 in 2492 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.-5T>C has been reported in the literature in individuals affected with or being tested for LQTS, without strong evidence for causality (Jongbloed_2002, Stattin_2012). These reports do not provide unequivocal conclusions about association of the variant with Arrhythmia. Co-occurrences with other pathogenic variant(s) have been reported (PKP2 c.235C>T, p.Arg79X), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, three classify as likely benign while two classify as VUS. Based on the evidence outlined above, the variant was classified as VUS - possibly benign.

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