ClinVar Miner

Submissions for variant NM_005751.5(AKAP9):c.6331-8T>C

gnomAD frequency: 0.00210  dbSNP: rs186211000
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000466560 SCV000563324 benign Long QT syndrome 2024-01-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001269124 SCV001448375 benign not specified 2020-11-30 criteria provided, single submitter clinical testing Variant summary: AKAP9 c.6331-8T>C 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. 4/4 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 0.00051 in 245330 control chromosomes, predominantly at a frequency of 0.0074 within the African or African-American subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 2220-fold the estimated maximal expected allele frequency for a pathogenic variant in AKAP9 causing Long QT Syndrome phenotype (3.3e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.6331-8T>C in individuals affected with Long QT Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and cited the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV001653855 SCV001866733 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002253457 SCV002524851 benign Long QT syndrome 11 2021-12-05 criteria provided, single submitter clinical testing

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