M-9698-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP7BA1
The ENST00000362079.2(MT-CO3):āc.492T>Cā(p.Leu164=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Mitomap GenBank:
š 0.040 ( AC: 2433 )
Consequence
MT-CO3
ENST00000362079.2 synonymous
ENST00000362079.2 synonymous
Scores
Clinical Significance
Not reported in ClinVar
No linked disesase in Mitomap
Conservation
PhyloP100: -16.0
Genes affected
MT-CO3 (HGNC:7422): (mitochondrially encoded cytochrome c oxidase III) Predicted to enable electron transfer activity and oxidoreduction-driven active transmembrane transporter activity. Involved in respiratory chain complex IV assembly. Part of respiratory chain complex IV. Implicated in MELAS syndrome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP7
Synonymous conserved (PhyloP=-16 with no splicing effect.
BA1
High frequency in mitomap database: 0.0398
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX3 | COX3.1 use as main transcript | c.492T>C | p.Leu164= | synonymous_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CO3 | ENST00000362079.2 | c.492T>C | p.Leu164= | synonymous_variant | 1/1 | P1 |
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
2433
Gnomad homoplasmic
AF:
AC:
2953
AN:
56410
Gnomad heteroplasmic
AF:
AC:
1
AN:
56410
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at