chrM-4850-C-T

Position:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Mitomap GenBank:
𝑓 0.013 ( AC: 787 )

Consequence

ND2
synonymous

Scores

Clinical Significance

Not reported in ClinVar
No linked disesase in Mitomap

Conservation

PhyloP100: -5.89
Variant links:
Genes affected
ND2 (HGNC:7456): (mitochondrially encoded NADH dehydrogenase 2) 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; multiple sclerosis; myocardial infarction; neurodegenerative disease (multiple); and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
High frequency in mitomap database: 0.0128999995

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ND2unassigned_transcript_4793 c.381C>T p.Gly127Gly synonymous_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons 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:
0.013
AC:
787
Gnomad homoplasmic
AF:
0.0020
AC:
111
AN:
56434
Gnomad heteroplasmic
AF:
0.0
AC:
0
AN:
56434
Alfa
AF:
0.000668
Hom.:
3

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

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: rs28413696; hg19: chrM-4851; API