chrM-15923-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The ENST00000387460.2(MT-TT):n.36A>G variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 0 )
Consequence
MT-TT
ENST00000387460.2 non_coding_transcript_exon
ENST00000387460.2 non_coding_transcript_exon
Scores
Mitotip
Uncertain
Clinical Significance
LIMM-/-MERRF-/-mito-disease
Conservation
PhyloP100: 8.59
Genes affected
MT-TT (HGNC:7499): (mitochondrially encoded tRNA threonine)
MT-CYB (HGNC:7427): (mitochondrially encoded cytochrome b) Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrion. Implicated in ovarian carcinoma 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 3 ACMG points.
PM2
?
Very low frequency in mitomap database: 0.0
PP5
?
Variant M-15923-A-G is Pathogenic according to our data. Variant chrM-15923-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 39575.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1, Uncertain_significance=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRNT | TRNT.1 use as main transcript | n.36A>G | non_coding_transcript_exon_variant | 1/1 | |||
CYTB | CYTB.1 use as main transcript | downstream_gene_variant | |||||
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.36A>G | non_coding_transcript_exon_variant | 1/1 | |||||
MT-CYB | ENST00000361789.2 | downstream_gene_variant | P1 | ||||||
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.
Mitomap GenBank
AF:
AC:
0
Alfa
AF:
Hom.:
Mitomap
LIMM-/-MERRF-/-mito-disease
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Mitochondrial disease Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Undiagnosed Diseases Network, NIH | Mar 13, 2019 | - - |
Variant of unknown significance Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Aug 01, 1992 | - - |
Constipation;C0022346:Jaundice;C0085298:Sudden cardiac death;C1848924:Infantile onset;C1855106:Neonatal onset;C1858120:Generalized hypotonia;C2315100:Failure to thrive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Sep 21, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
Hmtvar
Pathogenic
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at