M-10013-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4BP6_ModerateBS2
The ENST00000387429.1(MT-TG):n.23C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 1 )
Consequence
MT-TG
ENST00000387429.1 non_coding_transcript_exon
ENST00000387429.1 non_coding_transcript_exon
Scores
Mitotip
Benign
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 0.739
Genes affected
MT-TG (HGNC:7486): (mitochondrially encoded tRNA glycine)
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]
MT-CO3 (HGNC:7422): (mitochondrially encoded cytochrome c oxidase III) Predicted to enable electron transfer activity and oxidoreduction-driven active transmembrane transporter activity. Involved in respiratory chain complex IV assembly. Part of respiratory chain complex IV. Implicated in MELAS syndrome. [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.
PM2
Very low frequency in mitomap database: 0.0
BP4
Mitotip and hmtvar scores support benign criterium.
BP6
Variant M-10013-C-T is Benign according to our data. Variant chrM-10013-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 690097.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomadMitoHomoplasmic at 19
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNG | TRNG.1 use as main transcript | n.23C>T | non_coding_transcript_exon_variant | 1/1 | ||||
COX3 | COX3.1 use as main transcript | downstream_gene_variant | YP_003024032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MT-TG | ENST00000387429.1 | n.23C>T | non_coding_transcript_exon_variant | 1/1 | ||||||
MT-ND3 | ENST00000361227.2 | upstream_gene_variant | ENSP00000355206 | P1 | ||||||
MT-CO3 | ENST00000362079.2 | downstream_gene_variant | ENSP00000354982 | 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:
19
AN:
56433
Gnomad heteroplasmic
AF:
AC:
0
AN:
56433
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Benign:1
Likely 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.10013C>T variant in MT-TG gene is interpreted to be a Likely Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BP4 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Benign
Hmtvar
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at