chrM-10440-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The ENST00000387439.1(MT-TR):n.36T>C variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Benign (★).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 1 )
Consequence
MT-TR
ENST00000387439.1 non_coding_transcript_exon
ENST00000387439.1 non_coding_transcript_exon
Scores
Mitotip
Uncertain
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 4.82
Genes affected
MT-TR (HGNC:7496): (mitochondrially encoded tRNA arginine)
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-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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very low frequency in mitomap database: 0.0
BP6
Variant M-10440-T-C is Benign according to our data. Variant chrM-10440-T-C is described in ClinVar as [Benign]. Clinvar id is 690119.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNR | TRNR.1 use as main transcript | n.36T>C | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MT-TR | ENST00000387439.1 | n.36T>C | non_coding_transcript_exon_variant | 1/1 | ||||||
MT-ND4L | ENST00000361335.1 | upstream_gene_variant | ENSP00000354728 | P1 | ||||||
MT-ND3 | ENST00000361227.2 | downstream_gene_variant | ENSP00000355206 | P1 |
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
1
Gnomad homoplasmic
AF:
AC:
0
AN:
56420
Gnomad heteroplasmic
AF:
AC:
1
AN:
56420
Mitomap
No disease associated.
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Benign:1
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Jul 12, 2019 | The NC_012920.1:m.10440T>C variant in MT-TR gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BS4 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
Hmtvar
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at