chrM-7469-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
Variant has been reported in ClinVar as Benign (★).
Frequency
Mitomap GenBank:
𝑓 0.00020 ( AC: 12 )
Consequence
TRNS1
missense
missense
Scores
Mitotip
Benign
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 0.702
Genes affected
TRNS1 (HGNC:7497): (mitochondrially encoded tRNA serine 1 (UCN))
TRND (HGNC:7478): (mitochondrially encoded tRNA aspartic acid)
COX1 (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 Likely_benign. Variant got -2 ACMG points.
BP6
Variant M-7469-C-T is Benign according to our data. Variant chrM-7469-C-T is described in ClinVar as [Benign]. Clinvar id is 690027.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNS1 | unassigned_transcript_4800 | c.46G>A | p.Gly16Arg | missense_variant | 1/1 | |||
TRND | unassigned_transcript_4801 | c.-49C>T | upstream_gene_variant | |||||
COX1 | unassigned_transcript_4799 | c.*24C>T | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|
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:
12
Gnomad homoplasmic
AF:
AC:
2
AN:
56433
Gnomad heteroplasmic
AF:
AC:
1
AN:
56433
Mitomap
No disease associated.
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MELAS syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Jul 12, 2019 | The NC_012920.1:m.7469C>T variant in MT-TS1 gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BS2, BP4 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Benign
Hmtvar
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at