chr7-92098173-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_005751.5(AKAP9):āc.10672A>Gā(p.Ile3558Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000813 in 1,612,382 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005751.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AKAP9 | NM_005751.5 | c.10672A>G | p.Ile3558Val | missense_variant | Exon 43 of 50 | ENST00000356239.8 | NP_005742.4 | |
AKAP9 | NM_147185.3 | c.10648A>G | p.Ile3550Val | missense_variant | Exon 43 of 50 | NP_671714.1 | ||
AKAP9 | NM_001379277.1 | c.5317A>G | p.Ile1773Val | missense_variant | Exon 22 of 29 | NP_001366206.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000617 AC: 94AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000769 AC: 193AN: 250846Hom.: 0 AF XY: 0.000730 AC XY: 99AN XY: 135606
GnomAD4 exome AF: 0.000834 AC: 1217AN: 1460028Hom.: 2 Cov.: 29 AF XY: 0.000855 AC XY: 621AN XY: 726478
GnomAD4 genome AF: 0.000617 AC: 94AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | research | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | Jun 24, 2013 | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Congenital long QT syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 30, 2024 | Variant summary: AKAP9 c.10672A>G (p.Ile3558Val) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00077 in 250846 control chromosomes. The observed variant frequency is approximately 230-fold of the estimated maximal expected allele frequency for a pathogenic variant in AKAP9 causing Long QT Syndrome phenotype (3.3e-06). To our knowledge, c.10672A>G has been not been reported in the literature in individuals affected with Long QT Syndrome and no experimental evidence demonstrating an impact on protein function has been reported. ClinVar contains an entry for this variant (Variation ID: 191527). Based on the evidence outlined above, the variant was classified as likely benign. - |
AKAP9-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 10, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Arrhythmogenic right ventricular cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego | Apr 09, 2019 | - - |
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 23, 2025 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at