rs878888873

Variant names:

• chrM-10632-T-C
• rs878888873
• ENST00000361335.1:c.163T>C

Variant summary

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

The ENST00000361335.1(MT-ND4L):​c.163T>C​(p.Leu55Leu) 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 0.00090 (AC: 53)
• Consequence: MT-ND4L ENST00000361335.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -2.72
• Publications: 4 publications found

Genes affected

MT-ND4L (HGNC:7460): (mitochondrially encoded NADH 4L dehydrogenase) Predicted to enable NADH dehydrogenase (ubiquinone) activity. Predicted to be located in mitochondrial inner membrane. Implicated in Leber hereditary optic neuropathy and diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

MT-ND4 (HGNC:7459): (mitochondrially encoded NADH dehydrogenase 4) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Parkinson's disease; macular degeneration; and schizophrenia. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]

MT-ND3 (HGNC:7458): (mitochondrially encoded NADH dehydrogenase 3) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Leigh disease; and Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]

TRNR (HGNC:7496): (mitochondrially encoded tRNA arginine)

TRNR Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP6: Variant M-10632-T-C is Benign according to our data. Variant chrM-10632-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 376882.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.72 with no splicing effect.
• BS2: High AC in GnomadMitoHomoplasmic at 36

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ND4L	unassigned_transcript_4810	c.163T>C	p.Leu55Leu	synonymous_variant	Exon 1 of 1
ND4	unassigned_transcript_4811	c.-128T>C		upstream_gene_variant
ND3	unassigned_transcript_4808	c.*228T>C		downstream_gene_variant
TRNR	unassigned_transcript_4809	c.*163T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-ND4L	ENST00000361335.1	c.163T>C	p.Leu55Leu	synonymous_variant	Exon 1 of 1	6		ENSP00000354728.1
MT-ND4	ENST00000361381.2	c.-128T>C		upstream_gene_variant		6		ENSP00000354961.2
MT-ND3	ENST00000361227.2	c.*228T>C		downstream_gene_variant		6		ENSP00000355206.2
MT-TR	ENST00000387439.1	n.*163T>C		downstream_gene_variant		6

Frequencies

Mitomap GenBank AF: 0.00090 AC: 53

Gnomad homoplasmic AF: 0.00064 AC: 36 AN: 56432

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56432

Alfa AF: 0.00134 Hom.: 6

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 14, 2016

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

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.7
Mutation Taster		=95/5	polymorphism

Other links and lift over

dbSNP: rs878888873; hg19: chrM-10633;