chr9-128322868-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_016035.5(COQ4):c.10C>T(p.Leu4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000508 in 1,573,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L4L) has been classified as Likely benign.
Frequency
Consequence
NM_016035.5 synonymous
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 |
---|---|---|---|---|---|---|---|
COQ4 | NM_016035.5 | c.10C>T | p.Leu4= | synonymous_variant | 1/7 | ENST00000300452.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COQ4 | ENST00000300452.8 | c.10C>T | p.Leu4= | synonymous_variant | 1/7 | 1 | NM_016035.5 | P1 | |
COQ4 | ENST00000372875.3 | c.10C>T | p.Leu4= | synonymous_variant | 1/4 | 2 | |||
COQ4 | ENST00000608951.5 | c.10C>T | p.Leu4= | synonymous_variant | 1/3 | 2 | |||
COQ4 | ENST00000609948.1 | c.10C>T | p.Leu4= | synonymous_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183086Hom.: 0 AF XY: 0.0000393 AC XY: 4AN XY: 101820
GnomAD4 exome AF: 0.00000492 AC: 7AN: 1421648Hom.: 0 Cov.: 30 AF XY: 0.00000567 AC XY: 4AN XY: 705110
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at