M-9993-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000387429.1(MT-TG):n.3T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 0 )
Consequence
MT-TG
ENST00000387429.1 non_coding_transcript_exon
ENST00000387429.1 non_coding_transcript_exon
Scores
Mitotip
Uncertain
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 1.68
Genes affected
MT-TG (HGNC:7486): (mitochondrially encoded tRNA glycine)
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very low frequency in mitomap database: 0.0
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNG | TRNG.1 use as main transcript | n.3T>C | 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.3T>C | non_coding_transcript_exon_variant | 1/1 | ||||||
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:
0
Gnomad homoplasmic
AF:
AC:
2
AN:
56427
Gnomad heteroplasmic
AF:
AC:
2
AN:
56427
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Uncertain:1
Uncertain significance, 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.9993T>C variant in MT-TG gene is interpreted to be a Unknown Significance variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: PP3, PP6 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
Hmtvar
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at