rs201395766
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP6_Very_StrongBP7BS1BS2
The ENST00000361624.2(MT-CO1):c.357G>A(p.Glu119=) 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 0.0094 ( AC: 576 )
Consequence
MT-CO1
ENST00000361624.2 synonymous
ENST00000361624.2 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 1.21
Genes affected
MT-CO1 (HGNC:7419): (mitochondrially encoded cytochrome c oxidase I) Contributes to cytochrome-c oxidase activity. Predicted to be involved in electron transport coupled proton transport and mitochondrial electron transport, cytochrome c to oxygen. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP6
?
Variant M-6260-G-A is Benign according to our data. Variant chrM-6260-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 235511.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.21 with no splicing effect.
BS1
?
High frequency in mitomap database: 0.0094
BS2
?
High AC in GnomadMitoHomoplasmic at 777
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX1 | COX1.1 use as main transcript | c.357G>A | p.Glu119= | synonymous_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CO1 | ENST00000361624.2 | c.357G>A | p.Glu119= | 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:
576
Gnomad homoplasmic
AF:
AC:
777
AN:
56403
Gnomad heteroplasmic
AF:
AC:
10
AN:
56403
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 22, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 11, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at