chrM-7789-G-A

Variant names:

• chrM-7789-G-A
• rs386829014
• ENST00000361739.1:c.204G>A

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BS1 BS2

The ENST00000361739.1(MT-CO2):​c.204G>A​(p.Leu68Leu) 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 0.0085 (AC: 520)
• Consequence: MT-CO2 ENST00000361739.1 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2 No linked disesase in Mitomap
• Conservation: PhyloP100: -9.88
• Publications: 6 publications found

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]

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

TRND Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP6: Variant M-7789-G-A is Benign according to our data. Variant chrM-7789-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 376897.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: High frequency in mitomap database: 0.0085
• BS2: High AC in GnomadMitoHomoplasmic at 620

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COX2	unassigned_transcript_4802	c.204G>A	p.Leu68Leu	synonymous_variant	Exon 1 of 1
TRND	unassigned_transcript_4801	c.*204G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-CO2	ENST00000361739.1	c.204G>A	p.Leu68Leu	synonymous_variant	Exon 1 of 1	6		ENSP00000354876.1
MT-TD	ENST00000387419.1	n.*204G>A		downstream_gene_variant		6

Frequencies

Mitomap GenBank AF: 0.0085 AC: 520

Gnomad homoplasmic AF: 0.011 AC: 620 AN: 56423

Gnomad heteroplasmic AF: 0.000018 AC: 1 AN: 56423

Alfa AF: 0.00689 Hom.: 56

Mitomap

No disease associated.

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Feb 16, 2025

Laboratory of Genetics, Children's Clinical University Hospital Latvia

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Jan 26, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-9.9
Mutation Taster		=41/59	disease causing

Other links and lift over

dbSNP: rs386829014; hg19: chrM-7790;