rs9785013
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005751.5(AKAP9):c.5163-20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 1,570,554 control chromosomes in the GnomAD database, including 128,766 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005751.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.454 AC: 68922AN: 151872Hom.: 16861 Cov.: 32
GnomAD3 exomes AF: 0.391 AC: 97948AN: 250218Hom.: 20351 AF XY: 0.391 AC XY: 52930AN XY: 135374
GnomAD4 exome AF: 0.392 AC: 556095AN: 1418564Hom.: 111868 Cov.: 27 AF XY: 0.392 AC XY: 277698AN XY: 708534
GnomAD4 genome AF: 0.454 AC: 69017AN: 151990Hom.: 16898 Cov.: 32 AF XY: 0.451 AC XY: 33511AN XY: 74270
ClinVar
Submissions by phenotype
not specified Benign:5
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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Variant summary: AKAP9 c.5163-20G>A alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.39 in 250218 control chromosomes, predominantly at a frequency of 0.65 within the African or African-American subpopulation in the gnomAD database, including 3362 homozygotes. Therefore, suggesting the variant is the major allele observed in population(s) of African-American origin. A ClinVar submission (evaluation after 2014) cites the variant as benign. Based on the evidence outlined above, the variant was classified as benign. -
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Long QT syndrome 11 Benign:2
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not provided Benign:1
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Long QT syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at