ClinVar Miner

Submissions for variant NM_001148.6(ANK2):c.7488A>G (p.Thr2496=) (rs143161930)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000228062 SCV000286258 benign Long QT syndrome 2020-11-22 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001094920 SCV000447197 likely benign Cardiac arrhythmia, ankyrin B-related 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000602534 SCV000728917 likely benign not specified 2017-06-01 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000756995 SCV000885012 benign not provided 2018-05-15 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000602534 SCV000916449 benign not specified 2018-03-26 criteria provided, single submitter clinical testing Variant summary: ANK2 c.7488A>G alters a non-conserved nucleotide resulting in a synonymous change. The variant allele was found at a frequency of 0.0006 in 276162 control chromosomes, predominantly observed within the South Asian subpopulation at a frequency of 0.0041, including 3 homozygotes (in the gnomAD database). The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 410 fold of the estimated maximal expected allele frequency for a pathogenic variant in ANK2 causing Arrhythmia phenotype (1e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. To our knowledge, no occurrence of c.7488A>G in individuals affected with Arrhythmia 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. One laboratory classified the variant as benign, and the other laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as benign.

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