rs118203890
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000387460.2(MT-TT):n.63G>A 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:
Absent
Consequence
MT-TT
ENST00000387460.2 non_coding_transcript_exon
ENST00000387460.2 non_coding_transcript_exon
Scores
Mitotip
Uncertain
Clinical Significance
LHON-/-LHON-MS-/-dopaminergic-nerve-cell-death-(PD)-/-tic-disorder
Conservation
PhyloP100: 1.53
Genes affected
MT-TT (HGNC:7499): (mitochondrially encoded tRNA threonine)
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
No frequency data in Mitomap. Probably very rare.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRNT | TRNT.1 use as main transcript | n.63G>A | non_coding_transcript_exon_variant | 1/1 | |||
TRNP | TRNP.1 use as main transcript | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-TT | ENST00000387460.2 | n.63G>A | non_coding_transcript_exon_variant | 1/1 | |||||
MT-TP | ENST00000387461.2 | downstream_gene_variant |
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.
Gnomad homoplasmic
AF:
AC:
3
AN:
56430
Gnomad heteroplasmic
AF:
AC:
0
AN:
56430
Mitomap
LHON-/-LHON-MS-/-dopaminergic-nerve-cell-death-(PD)-/-tic-disorder
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1Other: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.15950G>A variant in MT-TT gene is interpreted to be a Unknown Significance variant based on the modified ACMG guidelines (unpublished).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, BP6 - |
Parkinson disease, mitochondrial Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 1999 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
Hmtvar
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at