rs199474819
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000387416.2(MT-TS1):n.42_43insG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Mitomap GenBank:
Absent
Consequence
MT-TS1
ENST00000387416.2 non_coding_transcript_exon
ENST00000387416.2 non_coding_transcript_exon
Scores
Clinical Significance
Not reported in ClinVar
No linked disesase in Mitomap
Conservation
PhyloP100: -1.71
Genes affected
MT-TS1 (HGNC:7497): (mitochondrially encoded tRNA serine 1 (UCN))
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 2 ACMG points.
PM2
?
No frequency data in Mitomap. Probably very rare.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRNS1 | TRNS1.1 use as main transcript | n.42_43insG | non_coding_transcript_exon_variant | 1/1 | |||
COX1 | COX1.1 use as main transcript | downstream_gene_variant | |||||
TRND | TRND.1 use as main transcript | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-TS1 | ENST00000387416.2 | n.42_43insG | non_coding_transcript_exon_variant | 1/1 | |||||
MT-CO1 | ENST00000361624.2 | downstream_gene_variant | P1 | ||||||
MT-TD | ENST00000387419.1 | upstream_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
No disease associated.
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at