M-14470-T-C

Variant names:

• chrM-14470-T-C
• rs3135030
• ENST00000361681.2:c.204A>G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP7 BA1

The ENST00000361681.2(MT-ND6):​c.204A>G​(p.Gly68Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G68G) has been classified as Likely benign.

• Frequency: Mitomap GenBank: 𝑓 0.019 (AC: 1137)
• Consequence: MT-ND6 ENST00000361681.2 synonymous
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -4.43
• Publications: 16 publications found

Genes affected

MT-ND6 (HGNC:7462): (mitochondrially encoded NADH dehydrogenase 6) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Predicted to be located in mitochondrial inner membrane. Implicated in Leber hereditary optic neuropathy; Leigh disease; and spinal muscular atrophy with lower extremity predominante 2B. [provided by Alliance of Genome Resources, Apr 2022]

TRNE (HGNC:7479): (mitochondrially encoded tRNA glutamic acid)

TRNE Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP7: Synonymous conserved (PhyloP=-4.43 with no splicing effect.
• BA1: High frequency in mitomap database: 0.0186

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361681.2. 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-ND6	ENST00000361681.2	TSL:6	c.204A>G	p.Gly68Gly	synonymous	Exon 1 of 1	ENSP00000354665.2	P03923
	MT-TE	ENST00000387459.1	TSL:6	n.*204A>G		downstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.019 AC: 1137

Gnomad homoplasmic AF: 0.016 AC: 882 AN: 56411

Gnomad heteroplasmic AF: 0.00012 AC: 7 AN: 56411

Alfa AF: 0.00901 Hom.: 102

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-4.4
Mutation Taster		=100/0	polymorphism

Other links and lift over

dbSNP: rs3135030; hg19: chrM-14471;