14-93347296-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182971.3(COX8C):c.28G>T(p.Ala10Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000312 in 1,604,678 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.28G>T | p.Ala10Ser | missense_variant | 1/2 | ENST00000342144.3 | |
UNC79 | NM_020818.5 | c.-351+13773G>T | intron_variant | ||||
UNC79 | XM_011537027.3 | c.-180+13773G>T | intron_variant | ||||
UNC79 | NR_144398.1 | n.325-732G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COX8C | ENST00000342144.3 | c.28G>T | p.Ala10Ser | missense_variant | 1/2 | 1 | NM_182971.3 | P1 | |
UNC79 | ENST00000256339.8 | c.-351+13773G>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000856 AC: 2AN: 233660Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129114
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1452496Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 722838
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.28G>T (p.A10S) alteration is located in exon 1 (coding exon 1) of the COX8C gene. This alteration results from a G to T substitution at nucleotide position 28, causing the alanine (A) at amino acid position 10 to be replaced by a serine (S). 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