rs386829022
Positions:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP7BS2
The ENST00000361739.1(MT-CO2):āc.462T>Cā(p.Ile154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Mitomap GenBank:
š 0.0010 ( AC: 62 )
Consequence
MT-CO2
ENST00000361739.1 synonymous
ENST00000361739.1 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -5.89
Genes affected
MT-CO2 (HGNC:7421): (mitochondrially encoded cytochrome c oxidase II) Contributes to cytochrome-c oxidase activity. Predicted to be involved in mitochondrial electron transport, cytochrome c to oxygen and positive regulation of vasoconstriction. Located in mitochondrial inner membrane. Part of respiratory chain complex IV. Biomarker of Huntington's disease and stomach cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP7
Synonymous conserved (PhyloP=-5.89 with no splicing effect.
BS2
High AC in GnomadMitoHomoplasmic at 57
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX2 | COX2.1 use as main transcript | c.462T>C | p.Ile154= | synonymous_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CO2 | ENST00000361739.1 | c.462T>C | p.Ile154= | 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:
62
Gnomad homoplasmic
AF:
AC:
57
AN:
56428
Gnomad heteroplasmic
AF:
AC:
0
AN:
56428
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Dec 22, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at