rs2853493

Positions:

• chrM-11467-A-G

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP6_Very_Strong BP7 BA1

The ENST00000361381.2(MT-ND4):​c.708A>G​(p.Leu236=) 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 0.13 (AC: 7901)
• Consequence: MT-ND4 ENST00000361381.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2 Altered-brain-pH-/-sCJD-patients
• Conservation: PhyloP100: -3.03

Genes affected

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]

ACMG classification

Verdict is Benign. Variant got -17 ACMG points.

• BP6: Variant M-11467-A-G is Benign according to our data. Variant chrM-11467-A-G is described in ClinVar as [Benign]. Clinvar id is 522716.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-3.03 with no splicing effect.
• BA1: High frequency in mitomap database: 0.1292

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-ND4	ENST00000361381.2	c.708A>G	p.Leu236=	synonymous_variant	1/1			P1

Frequencies

GnomAD4 exome Cov.: 0

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap GenBank AF: 0.13 AC: 7901

Gnomad homoplasmic AF: 0.16 AC: 8766 AN: 56343

Gnomad heteroplasmic AF: 0.000053 AC: 3 AN: 56343

Alfa AF: 0.259 Hom.: 1162

Mitomap

Altered-brain-pH-/-sCJD-patients

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

Mitochondrial disease Benign:1

Benign, criteria provided, single submitter

clinical testing

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Jul 20, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2853493; hg19: chrM-11468; COSMIC: COSV62294568; COSMIC: COSV62294568;