chrM-5951-A-G

Position:

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP6_Very_StrongBP7BA1

The ENST00000361624.2(MT-CO1):ā€‹c.48A>Gā€‹(p.Gly16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (ā˜…ā˜…).

Frequency

Mitomap GenBank:
š‘“ 0.011 ( AC: 645 )

Consequence

MT-CO1
ENST00000361624.2 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
No linked disesase in Mitomap

Conservation

PhyloP100: -3.38
Variant links:
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-5951-A-G is Benign according to our data. Variant chrM-5951-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 235783.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.38 with no splicing effect.
BA1
High frequency in mitomap database: 0.0106

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COX1COX1.1 use as main transcriptc.48A>G p.Gly16= synonymous_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-CO1ENST00000361624.2 linkuse as main transcriptc.48A>G p.Gly16= synonymous_variant 1/1 P1

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.011
AC:
645
Gnomad homoplasmic
AF:
0.027
AC:
1526
AN:
56418
Gnomad heteroplasmic
AF:
0.000053
AC:
3
AN:
56418
Alfa
AF:
0.00381
Hom.:
17

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 submitterclinical testingAthena DiagnosticsMay 25, 2018- -
Likely benign, criteria provided, single submitterclinical testingCenter for Pediatric Genomic Medicine, Children's Mercy Hospital and ClinicsAug 12, 2015- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7340122; hg19: chrM-5952; API