ClinVar Miner

Submissions for variant NM_000238.4(KCNH2):c.3331-13GT[2] (rs41313749)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000181747 SCV000234050 benign not specified 2013-03-19 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.
Invitae RCV000232365 SCV000283984 benign Long QT syndrome 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000232365 SCV000467503 likely benign Long QT syndrome 2016-06-14 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000181747 SCV000613855 benign not specified 2017-07-05 criteria provided, single submitter clinical testing
Color RCV000771154 SCV000902994 benign Arrhythmia 2018-03-15 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000181747 SCV001159573 benign not specified 2019-03-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000181747 SCV001364006 benign not specified 2019-09-03 criteria provided, single submitter clinical testing Variant summary: KCNH2 c.3331-9_3331-8delGT alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0037 in 161778 control chromosomes, predominantly at a frequency of 0.055 within the African or African-American subpopulation in the gnomAD database, including 19 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 550 fold of the estimated maximal expected allele frequency for a pathogenic variant in KCNH2 causing Arrhythmia phenotype (0.0001), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. Four ClinVar submitters (evaluation after 2014) cite the variant as benign (3x) and once as likely benign. Based on the evidence outlined above, the variant was classified as benign.

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