rs1057516061

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:
𝑓 0.0 ( AC: 3 )

Consequence

TRNS1
missense

Scores

Mitotip
Uncertain
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:2
Hearing-Loss

Conservation

PhyloP100: 1.64
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very low frequency in mitomap database: 0.0

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRNS1unassigned_transcript_4801 use as main transcriptc.19A>G p.Met7Val missense_variant 1/1
TRNDunassigned_transcript_4802 use as main transcriptc.-22T>C upstream_gene_variant
use as main transcript

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0
AC:
3
Gnomad homoplasmic
AF:
0.000053
AC:
3
AN:
56430
Gnomad heteroplasmic
AF:
0.0
AC:
0
AN:
56430

Mitomap

Hearing-Loss

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

MELAS syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineJul 12, 2019The NC_012920.1:m.7496T>C variant in MT-TS1 gene is interpreted to be a Unknown Significance variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: PP3, PP6 -
Myopathy Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingCenter for Neuroscience and Cell Biology, University of Coimbra, PortugalNov 21, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
13
Hmtvar
Benign
0.050

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1057516061; hg19: chrM-7497; API