rs397515728
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4BP6_Very_StrongBS2
The ENST00000387416.2(MT-TS1):n.22G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).
Frequency
Mitomap GenBank:
𝑓 0.0015 ( AC: 93 )
Consequence
MT-TS1
ENST00000387416.2 non_coding_transcript_exon
ENST00000387416.2 non_coding_transcript_exon
Scores
Mitotip
Benign
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -1.62
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 Benign. Variant got -13 ACMG points.
BP4
?
Mitotip and hmtvar scores support benign criterium.
BP6
?
Variant M-7493-C-T is Benign according to our data. Variant chrM-7493-C-T is described in ClinVar as [Benign]. Clinvar id is 42229.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomadMitoHomoplasmic at 13
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRNS1 | TRNS1.1 use as main transcript | n.22G>A | 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.22G>A | 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 GenBank
AF:
AC:
93
Gnomad homoplasmic
AF:
AC:
13
AN:
56433
Gnomad heteroplasmic
AF:
AC:
0
AN:
56433
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 10, 2015 | m.7493C>T in MTTS1: This variant is not expected to have clinical significance b ecause it has been identified in virtually all individuals from haplotypes D2a ( 60/60) and D2b (13/13) reported in MitoMap (http://www.mitomap.org/MITOMAP). - |
Juvenile myopathy, encephalopathy, lactic acidosis AND stroke 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.7493C>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