M-14476-G-A

Variant names:

• chrM-14476-G-A
• rs1057520103
• ENST00000361681.2:c.198C>T

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP6_Moderate BP7 BS2

The ENST00000361681.2(MT-ND6):​c.198C>T​(p.Val66Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.0031 (AC: 187)
• Consequence: MT-ND6 ENST00000361681.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -6.58
• Publications: 1 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 -7 ACMG points.

• BP6: Variant M-14476-G-A is Benign according to our data. Variant chrM-14476-G-A is described in ClinVar as Benign. ClinVar VariationId is 376998.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-6.58 with no splicing effect.
• BS2: High AC in GnomadMitoHomoplasmic at 46

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ND6	unassigned_transcript_4816	c.198C>T	p.Val66Val	synonymous_variant	Exon 1 of 1
TRNE	unassigned_transcript_4817	c.*198C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-ND6	ENST00000361681.2	c.198C>T	p.Val66Val	synonymous_variant	Exon 1 of 1	6		ENSP00000354665.2
MT-TE	ENST00000387459.1	n.*198C>T		downstream_gene_variant		6

Frequencies

Mitomap GenBank AF: 0.0031 AC: 187

Gnomad homoplasmic AF: 0.00082 AC: 46 AN: 56427

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56427

Alfa AF: 0.000779 Hom.: 3

Mitomap

No disease associated.

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 03, 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		-6.6

Other links and lift over

dbSNP: rs1057520103; hg19: chrM-14477; COSMIC: COSV104668816; COSMIC: COSV104668816;