chr14-93347282-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182971.3(COX8C):c.14G>A(p.Arg5His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,604,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182971.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX8C | NM_182971.3 | c.14G>A | p.Arg5His | missense_variant | 1/2 | ENST00000342144.3 | |
UNC79 | NM_020818.5 | c.-351+13759G>A | intron_variant | ||||
UNC79 | XM_011537027.3 | c.-180+13759G>A | intron_variant | ||||
UNC79 | NR_144398.1 | n.325-746G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COX8C | ENST00000342144.3 | c.14G>A | p.Arg5His | missense_variant | 1/2 | 1 | NM_182971.3 | P1 | |
UNC79 | ENST00000256339.8 | c.-351+13759G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000841 AC: 20AN: 237734Hom.: 0 AF XY: 0.000107 AC XY: 14AN XY: 130294
GnomAD4 exome AF: 0.000108 AC: 157AN: 1452426Hom.: 0 Cov.: 31 AF XY: 0.000122 AC XY: 88AN XY: 722612
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.14G>A (p.R5H) alteration is located in exon 1 (coding exon 1) of the COX8C gene. This alteration results from a G to A substitution at nucleotide position 14, causing the arginine (R) at amino acid position 5 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at