rs9783079
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2
The ENST00000361739.1(MT-CO2):c.282C>T(p.Ser94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Mitomap GenBank:
𝑓 0.0071 ( AC: 435 )
Consequence
MT-CO2
ENST00000361739.1 synonymous
ENST00000361739.1 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -12.6
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 Benign. Variant got -11 ACMG points.
BP6
Variant M-7867-C-T is Benign according to our data. Variant chrM-7867-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 235282.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-12.6 with no splicing effect.
BS1
High frequency in mitomap database: 0.0070999996
BS2
High AC in GnomadMitoHomoplasmic at 1484
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| COX2 | COX2.1 use as main transcript | c.282C>T | p.Ser94= | synonymous_variant | 1/1 | YP_003024029.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MT-CO2 | ENST00000361739.1 | c.282C>T | p.Ser94= | synonymous_variant | 1/1 | ENSP00000354876 | 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:
435
Gnomad homoplasmic
AF:
AC:
1484
AN:
56426
Gnomad heteroplasmic
AF:
AC:
1
AN:
56426
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 29, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at