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GeneBe

M-7624-T-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP6_ModerateBP7BS2

The ENST00000361739.1(MT-CO2):c.39T>A(p.Thr13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:
𝑓 0.0046 ( AC: 284 )

Consequence

MT-CO2
ENST00000361739.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.89
Variant links:
Genes affected
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-TD (HGNC:7478): (mitochondrially encoded tRNA aspartic acid)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant M-7624-T-A is Benign according to our data. Variant chrM-7624-T-A is described in ClinVar as [Benign]. Clinvar id is 805037.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.89 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomadMitoHomoplasmic at 1550

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COX2COX2.1 use as main transcriptc.39T>A p.Thr13= synonymous_variant 1/1
TRNDTRND.1 use as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-CO2ENST00000361739.1 linkuse as main transcriptc.39T>A p.Thr13= synonymous_variant 1/1 P1
MT-TDENST00000387419.1 linkuse as main transcript downstream_gene_variant

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0046
AC:
284
Gnomad homoplasmic
AF:
0.027
AC:
1550
AN:
56422
Gnomad heteroplasmic
AF:
0.0
AC:
0
AN:
56422
Alfa
AF:
0.00335
Hom.:
15

Mitomap

No disease associated.

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsNov 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs28358879; hg19: chrM-7625; API