rs140782750
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_005751.5(AKAP9):āc.7166A>Gā(p.Asp2389Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000112 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D2389D) has been classified as Likely benign.
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP9 | NM_005751.5 | c.7166A>G | p.Asp2389Gly | missense_variant | 31/50 | ENST00000356239.8 | |
AKAP9 | NM_147185.3 | c.7142A>G | p.Asp2381Gly | missense_variant | 31/50 | ||
AKAP9 | NM_001379277.1 | c.1811A>G | p.Asp604Gly | missense_variant | 10/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP9 | ENST00000356239.8 | c.7166A>G | p.Asp2389Gly | missense_variant | 31/50 | 1 | NM_005751.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000683 AC: 104AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000176 AC: 44AN: 250642Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135548
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461744Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727162
GnomAD4 genome ? AF: 0.000683 AC: 104AN: 152364Hom.: 0 Cov.: 32 AF XY: 0.000738 AC XY: 55AN XY: 74512
ClinVar
Submissions by phenotype
Long QT syndrome 11 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 26, 2018 | The AKAP9 c.7166A>G; p.Asp2389Gly variant (rs140782750), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 417034). This variant is found in the African population with an allele frequency of 0.23% (55/23,974 alleles) in the Genome Aggregation Database. The aspartic acid at codon 2389 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is tolerated. Due to limited information, the clinical significance of the p.Asp2389Gly variant is uncertain at this time. - |
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2019 | 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