Variant chrM-9993-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000387429.1(MT-TG):n.3T>C 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-TG
ENST00000387429.1 non_coding_transcript_exon

Scores

Mitotip

Uncertain

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

No linked disesase in Mitomap

Conservation

PhyloP100: 1.68

Variant links:

Genes affected

MT-TG (HGNC:7486): (mitochondrially encoded tRNA glycine)

MT-TG links:

TRNG (HGNC:):

TRNG links:

MT-CO3 (HGNC:7422): (mitochondrially encoded cytochrome c oxidase III) Predicted to enable electron transfer activity and oxidoreduction-driven active transmembrane transporter activity. Involved in respiratory chain complex IV assembly. Part of respiratory chain complex IV. Implicated in MELAS syndrome. [provided by Alliance of Genome Resources, Apr 2022]

MT-CO3 links:

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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	UniProt
TRNG	TRNG.1 use as main transcript	n.3T>C		non_coding_transcript_exon_variant	1/1
COX3	COX3.1 use as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-TG	ENST00000387429.1 linkuse as main transcript	n.3T>C		non_coding_transcript_exon_variant	1/1
MT-CO3	ENST00000362079.2 linkuse as main transcript			downstream_gene_variant				P1

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:

0.000035

AC:

AN:

56427

Gnomad heteroplasmic

AF:

0.000035

AC:

AN:

56427

Alfa

AF:

0.000223

Hom.:

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.9993T>C variant in MT-TG 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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction