dbSNP rs368623956: MT-CO2:p.Asp92Asp (chrM-7861-T-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2

The ENST00000361739.1(MT-CO2):c.276T>C(p.Asp92Asp) 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 0.0052 ( AC: 317 )

Consequence

MT-CO2
ENST00000361739.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: 0.125

Publications

5 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 Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
cytochrome-c oxidase deficiency disease
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
MELAS syndrome
Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet
Leigh syndrome
Inheritance: Mitochondrial Classification: LIMITED Submitted by: ClinGen

MT-CO2 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: Benign. The variant received -11 ACMG points.

BP6

Variant M-7861-T-C is Benign according to our data. Variant chrM-7861-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 235521.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.125 with no splicing effect.

BS1

High frequency in mitomap database: 0.0052

BS2

High AC in GnomadMitoHomoplasmic at 199

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.276T>C	p.Asp92Asp	synonymous	Exon 1 of 1	ENSP00000354876.1	P00403

Frequencies

Mitomap GenBank

AF:

0.0052

AC:

317

Gnomad homoplasmic

AF:

0.0035

AC:

199

AN:

56413

Gnomad heteroplasmic

AF:

0.00011

AC:

AN:

56413

Alfa

AF:

0.00410

Hom.:

Mitomap

No disease associated.

ClinVar

ClinVar submissions

Significance:Likely benign

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

0.13

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