Variant chrM-4311-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 ENST00000387365.1(MT-TI):n.49G>A variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:

𝑓 0.0 ( AC: 0 )

Consequence

MT-TI
ENST00000387365.1 non_coding_transcript_exon

Scores

Mitotip

Pathogenic

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

No linked disesase in Mitomap

Conservation

PhyloP100: 4.54

Variant links:

Genes affected

MT-TI (HGNC:7488): (mitochondrially encoded tRNA isoleucine)

MT-TI links:

TRNI (HGNC:):

TRNI links:

MT-ND1 (HGNC:7455): (mitochondrially encoded NADH dehydrogenase 1) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Located in mitochondrial membrane. Part of mitochondrial respiratory chain complex I. Implicated in several diseases, including MELAS syndrome; neurodegenerative disease (multiple); optic nerve disease (multiple); toxic shock syndrome; and type 2 diabetes mellitus. Biomarker of Alzheimer's disease; Parkinson's disease; and multiple sclerosis. [provided by Alliance of Genome Resources, Apr 2022]

MT-ND1 links:

MT-TQ (HGNC:7495): (mitochondrially encoded tRNA glutamine)

MT-TQ 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	Protein	UniProt
TRNI	TRNI.1 use as main transcript	n.49G>A		non_coding_transcript_exon_variant	1/1
TRNQ	TRNQ.1 use as main transcript			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein	Appris
MT-TI	ENST00000387365.1 linkuse as main transcript	n.49G>A	non_coding_transcript_exon_variant	1/1
MT-ND1	ENST00000361390.2 linkuse as main transcript		downstream_gene_variant		ENSP00000354687	P1
MT-TQ	ENST00000387372.1 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:

Mitomap

No disease associated.

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Mitochondrial disease

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 09, 2023

The MT-TI m.4311G>A mitochondrial variant has not, to our knowledge, been reported in the peer-reviewed literature. This variant is not observed in version 3.2.1 of the Genome Aggregation Database. Based on the available evidence, the m.4311G>A variant is classified as a variant of uncertain significance for primary mitochondrial disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mitotip

Pathogenic

Hmtvar

Benign

0.050

Splicing

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

Publications

No publications associated with this variant yet.