NM_005751.5:c.8665C>T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005751.5(AKAP9):c.8665C>T(p.Leu2889Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 1,603,034 control chromosomes in the GnomAD database, including 123,832 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005751.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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AKAP9 | NM_005751.5 | c.8665C>T | p.Leu2889Leu | synonymous_variant | Exon 34 of 50 | ENST00000356239.8 | NP_005742.4 | |
AKAP9 | NM_147185.3 | c.8641C>T | p.Leu2881Leu | synonymous_variant | Exon 34 of 50 | NP_671714.1 | ||
AKAP9 | NM_001379277.1 | c.3310C>T | p.Leu1104Leu | synonymous_variant | Exon 13 of 29 | NP_001366206.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.415 AC: 63008AN: 151840Hom.: 13531 Cov.: 32
GnomAD3 exomes AF: 0.378 AC: 94441AN: 250064Hom.: 18697 AF XY: 0.379 AC XY: 51352AN XY: 135352
GnomAD4 exome AF: 0.385 AC: 559267AN: 1451076Hom.: 110283 Cov.: 32 AF XY: 0.386 AC XY: 278704AN XY: 722482
GnomAD4 genome AF: 0.415 AC: 63078AN: 151958Hom.: 13549 Cov.: 32 AF XY: 0.412 AC XY: 30610AN XY: 74264
ClinVar
Submissions by phenotype
not specified Benign:5
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Long QT syndrome 11 Benign:2
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not provided Benign:1
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Congenital long QT syndrome Benign:1
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Long QT syndrome Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as 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