rs141228574
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_016035.5(COQ4):āc.483G>Cā(p.Glu161Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00811 in 1,613,374 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E161G) has been classified as Uncertain significance.
Frequency
Consequence
NM_016035.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COQ4 | NM_016035.5 | c.483G>C | p.Glu161Asp | missense_variant | 5/7 | ENST00000300452.8 | |
COQ4 | XM_047423449.1 | c.*83G>C | 3_prime_UTR_variant | 4/4 | |||
COQ4 | NM_001305942.2 | c.*3-1241G>C | intron_variant | ||||
COQ4 | XM_017014792.2 | c.*3-617G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COQ4 | ENST00000300452.8 | c.483G>C | p.Glu161Asp | missense_variant | 5/7 | 1 | NM_016035.5 | P1 | |
COQ4 | ENST00000461102.1 | n.1822G>C | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00556 AC: 846AN: 152174Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00629 AC: 1568AN: 249250Hom.: 9 AF XY: 0.00641 AC XY: 865AN XY: 134878
GnomAD4 exome AF: 0.00838 AC: 12239AN: 1461082Hom.: 85 Cov.: 31 AF XY: 0.00849 AC XY: 6168AN XY: 726752
GnomAD4 genome AF: 0.00555 AC: 845AN: 152292Hom.: 6 Cov.: 32 AF XY: 0.00532 AC XY: 396AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 05, 2016 | 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. - |
Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | COQ4: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at