ClinVar Miner

Submissions for variant NM_005751.4(AKAP9):c.8286A>C (p.Lys2762Asn) (rs144875383)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000171724 SCV000055233 likely benign not provided 2013-06-24 criteria provided, single submitter research
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000171724 SCV000229669 uncertain significance not provided 2015-01-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV000241571 SCV000319822 likely benign Cardiovascular phenotype 2019-01-10 criteria provided, single submitter clinical testing Subpopulation frequency in support of benign classification;In silico models in agreement (benign)
Invitae RCV001084749 SCV000563335 likely benign Long QT syndrome 2019-12-31 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000624954 SCV000743176 likely benign Long QT syndrome 11 2014-10-09 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV001192966 SCV001361459 benign not specified 2019-11-26 criteria provided, single submitter clinical testing Variant summary: AKAP9 c.8286A>C (p.Lys2762Asn) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.001 in 250844 control chromosomes, predominantly at a frequency of 0.0019 within the Non-Finnish European subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 190 fold higher than the estimated maximal expected allele frequency for a pathogenic variant in AKAP9 causing Arrhythmia phenotype (1e-05), strongly suggesting that the variant is a benign polymorphism. c.8286A>C has been reported in the literature in heterozygous individuals without ECG signs of Long QT Syndrome (Ghouse_2015). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three ClinVar submissions (evaluation after 2014) cite the variant twice as likely benign and once as uncertain significance. Based on the evidence outlined above, the variant was classified as benign.

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