ClinVar Miner

Submissions for variant NM_004519.4(KCNQ3):c.1800-12G>A

gnomAD frequency: 0.00001  dbSNP: rs761923188
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000431143 SCV000523128 likely benign not specified 2016-01-20 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002062553 SCV002352593 likely benign Benign neonatal seizures 2023-11-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000431143 SCV002819356 uncertain significance not specified 2022-12-08 criteria provided, single submitter clinical testing Variant summary: KCNQ3 c.1800-12G>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant weakens a canonical 3' acceptor site, whereas two predict the variant has no significant impact on splicing. These predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4e-06 in 251274 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1800-12G>A in individuals affected with Benign Familial Neonatal Seizures and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and both laboratories classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.

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