1-234378125-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001206641.3(COA6):c.372+3736C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 152,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Consequence
COA6
NM_001206641.3 intron
NM_001206641.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.78
Genes affected
COA6 (HGNC:18025): (cytochrome c oxidase assembly factor 6) This gene encodes a member of the cytochrome c oxidase subunit 6B family. The encoded protein associates with cytochrome c oxidase may act has an cytochrome c oxidase mitochondrial respiratory complex VI assembly factor. Mutations in this gene may be associated with fatal infantile cardiomyopathy. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| COA6 | NM_001206641.3 | c.372+3736C>T | intron_variant | ENST00000366615.10 | |||
| COA6 | NM_001012985.2 | c.282+3736C>T | intron_variant | ||||
| COA6 | NM_001301733.1 | c.144+3736C>T | intron_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| COA6 | ENST00000366615.10 | c.372+3736C>T | intron_variant | 1 | NM_001206641.3 | ||||
| COA6 | ENST00000366612.1 | c.144+3736C>T | intron_variant | 1 | P1 | ||||
| COA6 | ENST00000366613.1 | c.282+3736C>T | intron_variant | 1 | |||||
| COA6 | ENST00000619305.1 | c.144+3736C>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes 0.0000263 AC: 4AN: 151926Hom.: 0 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0000263 AC: 4AN: 152046Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74316
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at