dbSNP rs878853024: MT-CO2:p.Leu78Leu (chrM-7819-C-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000361739.1(MT-CO2):c.234C>A(p.Leu78Leu) 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 0.0040 ( AC: 245 )

Consequence

MT-CO2
ENST00000361739.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

No linked disesase in Mitomap

Conservation

PhyloP100: -20.0

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 links:

TRND (HGNC:7478): (mitochondrially encoded tRNA aspartic acid)

TRND Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: Mitochondrial Classification: MODERATE Submitted by: ClinGen

TRND links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP6

Variant M-7819-C-A is Benign according to our data. Variant chrM-7819-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 235379.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomadMitoHomoplasmic at 729

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.234C>A	p.Leu78Leu	synonymous	Exon 1 of 1	ENSP00000354876.1	P00403
	MT-TD	ENST00000387419.1	TSL:6	n.*234C>A		downstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.0040

AC:

245

Gnomad homoplasmic

AF:

0.013

AC:

729

AN:

56433

Gnomad heteroplasmic

AF:

0.0

AC:

AN:

56433

Alfa

AF:

0.00465

Hom.:

Mitomap

No disease associated.

ClinVar

ClinVar submissions as Germline

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

-20

Mutation Taster

=43/57

disease causing

(source)

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