rs150243147
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 4P and 9B. PM1PM2BP4_StrongBP6BS1
The NM_020247.5(COQ8A):āc.989A>Gā(p.Tyr330Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,610,946 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_020247.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COQ8A | NM_020247.5 | c.989A>G | p.Tyr330Cys | missense_variant | 8/15 | ENST00000366777.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COQ8A | ENST00000366777.4 | c.989A>G | p.Tyr330Cys | missense_variant | 8/15 | 1 | NM_020247.5 | P1 | |
COQ8A | ENST00000366778.5 | c.833A>G | p.Tyr278Cys | missense_variant | 8/15 | 1 | |||
COQ8A | ENST00000485462.5 | n.379A>G | non_coding_transcript_exon_variant | 4/11 | 1 | ||||
COQ8A | ENST00000478406.5 | n.968A>G | non_coding_transcript_exon_variant | 4/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00115 AC: 175AN: 152236Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000275 AC: 67AN: 243722Hom.: 0 AF XY: 0.000233 AC XY: 31AN XY: 132828
GnomAD4 exome AF: 0.000123 AC: 179AN: 1458592Hom.: 0 Cov.: 34 AF XY: 0.000110 AC XY: 80AN XY: 725536
GnomAD4 genome ? AF: 0.00115 AC: 175AN: 152354Hom.: 0 Cov.: 34 AF XY: 0.00111 AC XY: 83AN XY: 74508
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 08, 2021 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Nov 23, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | COQ8A: BS1 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 09, 2020 | - - |
COQ8A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 13, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at