chr4-83284851-T-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 4P and 16B. PVS1_StrongBP6_Very_StrongBS1BS2
The NM_015697.9(COQ2):c.64A>T(p.Arg22*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 1,546,968 control chromosomes in the GnomAD database, including 428 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015697.9 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0180 AC: 2737AN: 152194Hom.: 37 Cov.: 32
GnomAD3 exomes AF: 0.0180 AC: 2785AN: 154366Hom.: 24 AF XY: 0.0176 AC XY: 1482AN XY: 84120
GnomAD4 exome AF: 0.0222 AC: 30922AN: 1394660Hom.: 391 Cov.: 33 AF XY: 0.0219 AC XY: 15087AN XY: 689630
GnomAD4 genome AF: 0.0180 AC: 2736AN: 152308Hom.: 37 Cov.: 32 AF XY: 0.0176 AC XY: 1312AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:4
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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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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 198/11788=1.67% -
not provided Benign:3
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Coenzyme Q10 deficiency, primary, 1 Uncertain:1
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Coenzyme Q10 deficiency, primary, 1;C3714927:Multiple system atrophy 1, susceptibility to Benign:1
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Focal segmental glomerulosclerosis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at