rs121434469

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: 0 )

Consequence

TRNI
synonymous

Scores

Mitotip
Uncertain
13

Clinical Significance

Uncertain significance criteria provided, single submitter P:1U:1
Progressive-Encephalopathy-/-PEO+myopathy

Conservation

PhyloP100: 3.97
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
TRNIunassigned_transcript_4791 use as main transcriptc.28T>C p.Leu10Leu synonymous_variant 1/1
ND1unassigned_transcript_4790 use as main transcriptc.*28T>C downstream_gene_variant
TRNQunassigned_transcript_4792 use as main transcriptc.*39A>G downstream_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:
0
Gnomad homoplasmic
AF:
0.0
AC:
0
AN:
56425
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56425

Mitomap

Progressive-Encephalopathy-/-PEO+myopathy

ClinVar

Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Encephalopathy, familial progressive necrotizing Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMMay 01, 2004- -
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.4290T>C variant in MT-TI gene is interpreted to be a Unknown Significance variant based on the modified ACMG guidelines (unpublished).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, BS4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
13
Hmtvar
Pathogenic
1.0

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: rs121434469; hg19: chrM-4291; API