rs118203893
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The ENST00000387409.1(MT-TY):n.15G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Mitomap GenBank:
Absent
Consequence
MT-TY
ENST00000387409.1 non_coding_transcript_exon
ENST00000387409.1 non_coding_transcript_exon
Scores
Mitotip
Benign
Clinical Significance
CPEO
Conservation
PhyloP100: 1.50
Genes affected
MT-TY (HGNC:7502): (mitochondrially encoded tRNA tyrosine)
MT-CO1 (HGNC:7419): (mitochondrially encoded cytochrome c oxidase I) Contributes to cytochrome-c oxidase activity. Predicted to be involved in electron transport coupled proton transport and mitochondrial electron transport, cytochrome c to oxygen. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
No frequency data in Mitomap. Probably very rare.
PP5
?
Variant M-5877-C-T is Pathogenic according to our data. Variant chrM-5877-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 9552.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRNY | TRNY.1 use as main transcript | n.15G>A | non_coding_transcript_exon_variant | 1/1 | |||
COX1 | COX1.1 use as main transcript | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-TY | ENST00000387409.1 | n.15G>A | non_coding_transcript_exon_variant | 1/1 | |||||
MT-CO1 | ENST00000361624.2 | upstream_gene_variant | 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
CPEO
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Kearns-Sayre syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2001 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Benign
Hmtvar
Pathogenic
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at