rs1057520103

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrM-14476-G-A
• chrM-14476-G-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

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.198C>T	p.Val66Val	synonymous	Exon 1 of 1	ENSP00000354665.2	P03923
	MT-TE	ENST00000387459.1	TSL:6	n.*198C>T		downstream_gene	N/A

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

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-6.6

Other links and lift over

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