Variant chrM-8302-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The ENST00000387421.1(MT-TK):n.8A>G variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Mitomap GenBank:

𝑓 0.00010 ( AC: 6 )

Consequence

MT-TK
ENST00000387421.1 non_coding_transcript_exon

Scores

Mitotip

Benign

5.4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

No linked disesase in Mitomap

Conservation

PhyloP100: 4.75

Variant links:

Genes affected

MT-TK (HGNC:7489): (mitochondrially encoded tRNA lysine)

MT-TK links:

TRNK (HGNC:):

TRNK links:

MT-CO2 (HGNC:7421): (mitochondrially encoded cytochrome c oxidase II) Contributes to cytochrome-c oxidase activity. Predicted to be involved in mitochondrial electron transport, cytochrome c to oxygen and positive regulation of vasoconstriction. Located in mitochondrial inner membrane. Part of respiratory chain complex IV. Biomarker of Huntington's disease and stomach cancer. [provided by Alliance of Genome Resources, Apr 2022]

MT-CO2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Mitotip and hmtvar scores support benign criterium.

BS2

High AC in GnomadMitoHomoplasmic at 7

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRNK	TRNK.1 use as main transcript	n.8A>G		non_coding_transcript_exon_variant	1/1
COX2	COX2.1 use as main transcript			downstream_gene_variant			YP_003024029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-TK	ENST00000387421.1 linkuse as main transcript	n.8A>G		non_coding_transcript_exon_variant	1/1
MT-CO2	ENST00000361739.1 linkuse as main transcript			downstream_gene_variant				ENSP00000354876	P1

Frequencies

GnomAD4 exome

Cov.:

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

Mitomap GenBank

AF:

0.00010

AC:

Gnomad homoplasmic

AF:

0.00012

AC:

AN:

56434

Gnomad heteroplasmic

AF:

0.000018

AC:

AN:

56434

Mitomap

No disease associated.

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Athena Diagnostics

Jan 27, 2023

Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is uninformative in assessment of its pathogenicity (http://gnomad.broadinstitute.org). RNA splicing is not expected during the normal processing of this gene, therefore computational splicing tools were not utilized to evaluate this variant. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mitotip

Benign

5.4

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Mitomap

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over