rs28416101

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP7BS2

The ENST00000361390.2(MT-ND1):ā€‹c.30T>Cā€‹(p.Ile10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Mitomap GenBank:
š‘“ 0.0037 ( AC: 226 )

Consequence

MT-ND1
ENST00000361390.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar
Carotid-atherosclerosis-risk

Conservation

PhyloP100: -5.56
Variant links:
Genes affected
MT-ND1 (HGNC:7455): (mitochondrially encoded NADH dehydrogenase 1) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Located in mitochondrial membrane. Part of mitochondrial respiratory chain complex I. Implicated in several diseases, including MELAS syndrome; neurodegenerative disease (multiple); optic nerve disease (multiple); toxic shock syndrome; and type 2 diabetes mellitus. Biomarker of Alzheimer's disease; Parkinson's disease; and multiple sclerosis. [provided by Alliance of Genome Resources, Apr 2022]
MT-TL1 (HGNC:7490): (mitochondrially encoded tRNA leucine 1 (UUA/G)) Implicated in cardiomyopathy. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP7
Synonymous conserved (PhyloP=-5.56 with no splicing effect.
BS2
High AC in GnomadMitoHomoplasmic at 169

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRNL1TRNL1.1 use as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-ND1ENST00000361390.2 linkuse as main transcriptc.30T>C p.Ile10= synonymous_variant 1/1 P1
MT-TL1ENST00000386347.1 linkuse as main transcript downstream_gene_variant

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0037
AC:
226
Gnomad homoplasmic
AF:
0.0030
AC:
169
AN:
56429
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56429
Alfa
AF:
0.00244
Hom.:
20

Mitomap

Carotid-atherosclerosis-risk

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: rs28416101; hg19: chrM-3337; API