dbSNP rs386829022: MT-CO2:p.Ile154Ile (chrM-8047-T-C) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP7BS2

The ENST00000361739.1(MT-CO2):c.462T>C(p.Ile154Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:

𝑓 0.0010 ( AC: 62 )

Consequence

MT-CO2
ENST00000361739.1 synonymous

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

No linked disesase in Mitomap

Conservation

PhyloP100: -5.89

Publications

1 publications found

Variant links:

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]

MT-CO2 links:

TRNK (HGNC:7489): (mitochondrially encoded tRNA lysine)

TRNK Gene-Disease associations (from GenCC):

Leigh syndrome
Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
mitochondrial disease
Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
maternally-inherited cardiomyopathy and hearing loss
Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet
MERRF syndrome
Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet

TRNK links:

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new If you want to explore the variant's impact on the transcript ENST00000361739.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP7

Synonymous conserved (PhyloP=-5.89 with no splicing effect.

BS2

High AC in GnomadMitoHomoplasmic at 57

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361739.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-CO2	ENST00000361739.1	TSL:6	c.462T>C	p.Ile154Ile	synonymous	Exon 1 of 1	ENSP00000354876.1	P00403
	MT-TK	ENST00000387421.1	TSL:6	n.-248T>C		upstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.0010

AC:

Gnomad homoplasmic

AF:

0.0010

AC:

AN:

56428

Gnomad heteroplasmic

AF:

0.0

AC:

AN:

56428

Alfa

AF:

0.000111

Hom.:

Mitomap

No disease associated.

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-5.9

Mutation Taster

=71/29

polymorphism

(source)

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Mitomap

ClinVar

Computational scores

Publications

Other links and lift over