chr17-19909228-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007202.4(AKAP10):c.1936A>G(p.Ile646Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 1,612,096 control chromosomes in the GnomAD database, including 125,833 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_007202.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP10 | NM_007202.4 | c.1936A>G | p.Ile646Val | missense_variant | 14/15 | ENST00000225737.11 | |
AKAP10 | NM_001330152.2 | c.1762A>G | p.Ile588Val | missense_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP10 | ENST00000225737.11 | c.1936A>G | p.Ile646Val | missense_variant | 14/15 | 1 | NM_007202.4 | P1 | |
AKAP10 | ENST00000395536.7 | c.1762A>G | p.Ile588Val | missense_variant | 13/14 | 5 | |||
AKAP10 | ENST00000578898.1 | c.*269A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 3 | ||||
AKAP10 | ENST00000583951.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.427 AC: 64970AN: 151984Hom.: 14728 Cov.: 33
GnomAD3 exomes AF: 0.371 AC: 93016AN: 250460Hom.: 18352 AF XY: 0.364 AC XY: 49250AN XY: 135416
GnomAD4 exome AF: 0.385 AC: 562722AN: 1459994Hom.: 111071 Cov.: 37 AF XY: 0.382 AC XY: 277236AN XY: 726326
GnomAD4 genome ? AF: 0.428 AC: 65059AN: 152102Hom.: 14762 Cov.: 33 AF XY: 0.424 AC XY: 31542AN XY: 74368
ClinVar
Submissions by phenotype
Cardiac conduction defect, susceptibility to Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | May 15, 2007 | - - |
AKAP10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at