rs2853493

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

Variant has been reported in ClinVar as Benign (★★).

Frequency

Mitomap GenBank:
𝑓 0.13 ( AC: 7901 )

Consequence

ND4
synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2
Altered-brain-pH-/-sCJD-patients

Conservation

PhyloP100: -3.03
Variant links:
Genes affected
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 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.
BA1
High frequency in mitomap database: 0.1292

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ND4unassigned_transcript_4811 c.708A>G p.Leu236Leu synonymous_variant Exon 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

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
LINK: link

Submissions by phenotype

not specified Benign:1
May 04, 2022
Mendelics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mitochondrial disease Benign:1
Jul 20, 2024
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

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