14-103563041-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001370595.2(COA8):āc.40C>Gā(p.Pro14Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 1,541,778 control chromosomes in the GnomAD database, including 85,328 homozygotes. 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 Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P14T) has been classified as Likely benign.
Frequency
Consequence
NM_001370595.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COA8 | NM_001370595.2 | c.40C>G | p.Pro14Ala | missense_variant | Exon 1 of 5 | ENST00000409074.8 | NP_001357524.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COA8 | ENST00000409074.8 | c.40C>G | p.Pro14Ala | missense_variant | Exon 1 of 5 | 1 | NM_001370595.2 | ENSP00000386485.3 | ||
ENSG00000256500 | ENST00000472726.3 | c.40C>G | p.Pro14Ala | missense_variant | Exon 1 of 18 | 2 | ENSP00000439065.2 |
Frequencies
GnomAD3 genomes AF: 0.304 AC: 46261AN: 152070Hom.: 7315 Cov.: 34
GnomAD3 exomes AF: 0.258 AC: 37220AN: 144426Hom.: 5619 AF XY: 0.264 AC XY: 20884AN XY: 79108
GnomAD4 exome AF: 0.329 AC: 456649AN: 1389590Hom.: 78011 Cov.: 38 AF XY: 0.327 AC XY: 224491AN XY: 686606
GnomAD4 genome AF: 0.304 AC: 46278AN: 152188Hom.: 7317 Cov.: 34 AF XY: 0.297 AC XY: 22089AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
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. -
Mitochondrial complex 4 deficiency, nuclear type 17 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at