rs142263098
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000356239.8(AKAP9):c.5404G>A(p.Asp1802Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,613,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000356239.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AKAP9 | NM_005751.5 | c.5404G>A | p.Asp1802Asn | missense_variant | 22/50 | ENST00000356239.8 | NP_005742.4 | |
AKAP9 | NM_147185.3 | c.5404G>A | p.Asp1802Asn | missense_variant | 22/50 | NP_671714.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AKAP9 | ENST00000356239.8 | c.5404G>A | p.Asp1802Asn | missense_variant | 22/50 | 1 | NM_005751.5 | ENSP00000348573 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 40AN: 250964Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135636
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461284Hom.: 0 Cov.: 31 AF XY: 0.0000647 AC XY: 47AN XY: 726944
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 19, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2020 | 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