ClinVar Miner

Submissions for variant NM_000218.3(KCNQ1):c.683+3G>A

gnomAD frequency: 0.00003  dbSNP: rs1025802726
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV001843299 SCV001353247 likely benign Cardiac arrhythmia 2018-11-16 criteria provided, single submitter clinical testing
Invitae RCV001859118 SCV002160621 uncertain significance Long QT syndrome 2023-12-19 criteria provided, single submitter clinical testing This sequence change falls in intron 4 of the KCNQ1 gene. It does not directly change the encoded amino acid sequence of the KCNQ1 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KCNQ1-related conditions. ClinVar contains an entry for this variant (Variation ID: 924982). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV003293952 SCV004007862 uncertain significance Cardiovascular phenotype 2023-03-23 criteria provided, single submitter clinical testing The c.683+3G>A intronic variant results from a G to A substitution 3 nucleotides after coding exon 4 in the KCNQ1 gene. This nucleotide position is poorly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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