rs187255726
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_005751.5(AKAP9):c.2609G>A(p.Cys870Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000559 in 1,610,596 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. C870C) 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.2609G>A | p.Cys870Tyr | missense_variant | 8/50 | ENST00000356239.8 | |
AKAP9 | NM_147185.3 | c.2609G>A | p.Cys870Tyr | missense_variant | 8/50 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP9 | ENST00000356239.8 | c.2609G>A | p.Cys870Tyr | missense_variant | 8/50 | 1 | NM_005751.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000208 AC: 51AN: 245368Hom.: 0 AF XY: 0.000203 AC XY: 27AN XY: 133186
GnomAD4 exome AF: 0.0000549 AC: 80AN: 1458442Hom.: 0 Cov.: 35 AF XY: 0.0000565 AC XY: 41AN XY: 725372
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74412
ClinVar
Submissions by phenotype
Long QT syndrome 11 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 19, 2021 | - - |
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 28, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 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