rs975290833
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005751.5(AKAP9):c.6170C>T(p.Ala2057Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000248 in 1,611,498 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A2057A) has been classified as Likely benign.
Frequency
Consequence
NM_005751.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP9 | NM_005751.5 | c.6170C>T | p.Ala2057Val | missense_variant | 25/50 | ENST00000356239.8 | |
AKAP9 | NM_147185.3 | c.6170C>T | p.Ala2057Val | missense_variant | 25/50 | ||
AKAP9 | NM_001379277.1 | c.815C>T | p.Ala272Val | missense_variant | 4/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP9 | ENST00000356239.8 | c.6170C>T | p.Ala2057Val | missense_variant | 25/50 | 1 | NM_005751.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151838Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459660Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726098
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151838Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74124
ClinVar
Submissions by phenotype
Long QT syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 07, 2017 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with AKAP9-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with valine at codon 2057 of the AKAP9 protein (p.Ala2057Val). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and valine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at