M-10018-A-G

Position:

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2

The ENST00000387429.1(MT-TG):​n.28A>G variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:
𝑓 0.00010 ( AC: 9 )

Consequence

MT-TG
ENST00000387429.1 non_coding_transcript_exon

Scores

Mitotip
Uncertain
11

Clinical Significance

Benign criteria provided, single submitter B:1O:1
No linked disesase in Mitomap

Conservation

PhyloP100: 5.99
Variant links:
Genes affected
MT-TG (HGNC:7486): (mitochondrially encoded tRNA glycine)
MT-ND3 (HGNC:7458): (mitochondrially encoded NADH dehydrogenase 3) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Leigh disease; and Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Mitotip and hmtvar scores support benign criterium.
BP6
Variant M-10018-A-G is Benign according to our data. Variant chrM-10018-A-G is described in ClinVar as [Benign]. Clinvar id is 440974.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomadMitoHomoplasmic at 10

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRNGTRNG.1 use as main transcriptn.28A>G non_coding_transcript_exon_variant 1/1
COX3COX3.1 use as main transcript downstream_gene_variant YP_003024032.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MT-TGENST00000387429.1 linkuse as main transcriptn.28A>G non_coding_transcript_exon_variant 1/1
MT-ND3ENST00000361227.2 linkuse as main transcript upstream_gene_variant ENSP00000355206 P1
MT-CO3ENST00000362079.2 linkuse as main transcript downstream_gene_variant ENSP00000354982 P1

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.00010
AC:
9
Gnomad homoplasmic
AF:
0.00018
AC:
10
AN:
56433
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56433

Mitomap

No disease associated.

ClinVar

Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Benign:1
Benign, criteria provided, single submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineJul 12, 2019The NC_012920.1:m.10018A>G variant in MT-TG gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BS4 -
not provided Other:1
not provided, no classification providedphenotyping onlyGenomeConnect, ClinGen-GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
11
Hmtvar
Benign
0.15

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: rs1556423757; hg19: chrM-10019; API