rs387906736
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The ENST00000387382.1(MT-TW):n.45G>A variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 0 )
Consequence
MT-TW
ENST00000387382.1 non_coding_transcript_exon
ENST00000387382.1 non_coding_transcript_exon
Scores
Mitotip
Uncertain
Clinical Significance
Combined-OXPHOS-defects,Mito-encephalomyopathy
Conservation
PhyloP100: 4.97
Genes affected
MT-TW (HGNC:7501): (mitochondrially encoded tRNA tryptophan)
MT-ND2 (HGNC:7456): (mitochondrially encoded NADH dehydrogenase 2) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; multiple sclerosis; myocardial infarction; neurodegenerative disease (multiple); and urinary bladder cancer. [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 3 ACMG points.
PM2
?
Very low frequency in mitomap database: 0.0
PP5
?
Variant M-5556-G-A is Pathogenic according to our data. Variant chrM-5556-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 30007.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRNW | TRNW.1 use as main transcript | n.45G>A | non_coding_transcript_exon_variant | 1/1 | |||
TRNA | TRNA.1 use as main transcript | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-TW | ENST00000387382.1 | n.45G>A | non_coding_transcript_exon_variant | 1/1 | |||||
MT-ND2 | ENST00000361453.3 | downstream_gene_variant | P1 | ||||||
MT-TA | ENST00000387392.1 | 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.
Mitomap GenBank
AF:
AC:
0
Mitomap
Combined-OXPHOS-defects,Mito-encephalomyopathy
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Mitochondrial encephalomyopathy Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2010 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
Hmtvar
Pathogenic
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at