Variant chrM-5791-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000387405.1(MT-TC):n.36C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:

𝑓 0.0 ( AC: 0 )

Consequence

MT-TC
ENST00000387405.1 non_coding_transcript_exon

Scores

Mitotip

Uncertain

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

No linked disesase in Mitomap

Conservation

PhyloP100: 1.47

Variant links:

Genes affected

MT-TC (HGNC:7477): (mitochondrially encoded tRNA cysteine)

MT-TC links:

TRNC (HGNC:):

TRNC links:

MT-TY (HGNC:7502): (mitochondrially encoded tRNA tyrosine)

MT-TY links:

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
TRNC	TRNC.1 use as main transcript	n.36C>T		non_coding_transcript_exon_variant	1/1
TRNY	TRNY.1 use as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-TC	ENST00000387405.1 linkuse as main transcript	n.36C>T		non_coding_transcript_exon_variant	1/1
MT-TY	ENST00000387409.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD4 exome

Cov.:

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap GenBank

AF:

0.0

AC:

Gnomad homoplasmic

AF:

0.0

AC:

AN:

56427

Gnomad heteroplasmic

AF:

0.000018

AC:

AN:

56427

Mitomap

No disease associated.

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Juvenile myopathy, encephalopathy, lactic acidosis AND stroke

Uncertain:1

Uncertain significance, 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.5791G>A variant in MT-TC gene is interpreted to be a Unknown Significance variant based on the modified ACMG guidelines (unpublished).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, PP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction