rs878853022
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BA1
The ENST00000362079.2(MT-CO3):āc.339A>Gā(p.Gly113=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Mitomap GenBank:
š 0.046 ( AC: 2796 )
Consequence
MT-CO3
ENST00000362079.2 synonymous
ENST00000362079.2 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -5.39
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 -11 ACMG points.
BP6
?
Variant M-9545-A-G is Benign according to our data. Variant chrM-9545-A-G is described in ClinVar as [Benign]. Clinvar id is 235374.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-5.39 with no splicing effect.
BA1
?
High frequency in mitomap database: 0.045700002
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX3 | COX3.1 use as main transcript | c.339A>G | p.Gly113= | synonymous_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CO3 | ENST00000362079.2 | c.339A>G | p.Gly113= | 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:
2796
Gnomad homoplasmic
AF:
AC:
1170
AN:
56414
Gnomad heteroplasmic
AF:
AC:
4
AN:
56414
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 17, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at