rs387906418
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The ENST00000387382.1(MT-TW):n.34C>T variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Mitomap GenBank:
Absent
Consequence
MT-TW
ENST00000387382.1 non_coding_transcript_exon
ENST00000387382.1 non_coding_transcript_exon
Scores
Mitotip
Uncertain
Clinical Significance
HCM-severe-multisystem-disorder
Conservation
PhyloP100: 4.72
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
No frequency data in Mitomap. Probably very rare.
PP3
?
Mitotip and hmtvar scores support pathogenic criterium.
PP5
?
Variant M-5545-C-T is Pathogenic according to our data. Variant chrM-5545-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 9558.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.34C>T | 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.34C>T | 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
HCM-severe-multisystem-disorder
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Encephalocardiomyopathy, mitochondrial Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 15, 2008 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
Hmtvar
Pathogenic
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at