M-10005-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.15A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:
𝑓 0.00040 ( AC: 22 )

Consequence

MT-TG
ENST00000387429.1 non_coding_transcript_exon

Scores

Mitotip
Benign
3.7

Clinical Significance

Benign criteria provided, single submitter B:1
Hearing-loss-patient

Conservation

PhyloP100: 1.69
Variant links:
Genes affected
MT-TG (HGNC:7486): (mitochondrially encoded tRNA glycine)
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-10005-A-G is Benign according to our data. Variant chrM-10005-A-G is described in ClinVar as [Benign]. Clinvar id is 690092.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomadMitoHomoplasmic at 16

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRNGTRNG.1 use as main transcriptn.15A>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.15A>G non_coding_transcript_exon_variant 1/1
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:
0.00040
AC:
22
Gnomad homoplasmic
AF:
0.00028
AC:
16
AN:
56432
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56432
Alfa
AF:
0.00156
Hom.:
7

Mitomap

Hearing-loss-patient

ClinVar

Significance: Benign
Submissions summary: Benign: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.10005A>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, BS2, BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mitotip
Benign
3.7
Hmtvar
Benign
0.20

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: rs1603222621; hg19: chrM-10006; API