rs553800160
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_005751.5(AKAP9):āc.7773A>Cā(p.Gln2591His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000382 in 1,613,832 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP9 | NM_005751.5 | c.7773A>C | p.Gln2591His | missense_variant | 31/50 | ENST00000356239.8 | |
AKAP9 | NM_147185.3 | c.7749A>C | p.Gln2583His | missense_variant | 31/50 | ||
AKAP9 | NM_001379277.1 | c.2418A>C | p.Gln806His | missense_variant | 10/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP9 | ENST00000356239.8 | c.7773A>C | p.Gln2591His | missense_variant | 31/50 | 1 | NM_005751.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 34AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000769 AC: 193AN: 250908Hom.: 4 AF XY: 0.00105 AC XY: 142AN XY: 135706
GnomAD4 exome AF: 0.000399 AC: 583AN: 1461478Hom.: 9 Cov.: 32 AF XY: 0.000587 AC XY: 427AN XY: 727004
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74528
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | Jun 24, 2013 | - - |
Long QT syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 18, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2021 | 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