ENST00000361624.2:c.168T>C

Variant names:

• chrM-6071-T-C
• rs7340086
• ENST00000361624.2:c.168T>C

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP6_Very_Strong BP7 BA1

The ENST00000361624.2(MT-CO1):​c.168T>C​(p.Val56Val) 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 0.011 (AC: 653)
• Consequence: MT-CO1 ENST00000361624.2 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2 No linked disesase in Mitomap
• Conservation: PhyloP100: -10.7
• Publications: 3 publications found

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]

TRNC (HGNC:7477): (mitochondrially encoded tRNA cysteine)

TRNY (HGNC:7502): (mitochondrially encoded tRNA tyrosine)

TRNY Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP6: Variant M-6071-T-C is Benign according to our data. Variant chrM-6071-T-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 235696.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-10.7 with no splicing effect.
• BA1: High frequency in mitomap database: 0.0107

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361624.2. 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-CO1	ENST00000361624.2	TSL:6	c.168T>C	p.Val56Val	synonymous	Exon 1 of 1	ENSP00000354499.2
	MT-TC	ENST00000387405.1	TSL:6	n.-245A>G		upstream_gene	N/A
	MT-TY	ENST00000387409.1	TSL:6	n.-180A>G		upstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.011 AC: 653

Gnomad homoplasmic AF: 0.027 AC: 1532 AN: 56414

Gnomad heteroplasmic AF: 0.000035 AC: 2 AN: 56414

Alfa AF: 0.00391 Hom.: 17

Mitomap

No disease associated.

ClinVar

ClinVar submissions as Germline

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-11
Mutation Taster		=74/26	polymorphism

Other links and lift over

dbSNP: rs7340086; hg19: chrM-6072;