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GeneBe

rs2248727

chrM-9540-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6BP7BA1

The ENST00000362079.2(MT-CO3):c.334T>C(p.Leu112=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Mitomap GenBank:
𝑓 0.31 ( AC: 19089 )

Consequence

MT-CO3
ENST00000362079.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1
No linked disesase in Mitomap

Conservation

PhyloP100: -1.96
Variant links:
Genes affected
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 -10 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-9540-T-C is Benign according to our data. Variant chrM-9540-T-C is described in ClinVar as [Benign]. Clinvar id is 3027421.Status of the report is no_assertion_criteria_provided, 0 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=-1.96 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
High frequency in mitomap database: 0.31219998

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COX3COX3.1 use as main transcriptc.334T>C p.Leu112= synonymous_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-CO3ENST00000362079.2 linkuse as main transcriptc.334T>C p.Leu112= synonymous_variant 1/1 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:
0.31
AC:
19089
Gnomad homoplasmic
AF:
0.30
AC:
17141
AN:
56323
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56323
Alfa
AF:
0.0633
Hom.:
2367

Mitomap

No disease associated.

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Venous thromboembolism Benign:1
Benign, no assertion criteria providedcase-controlGenomics Division, Defence Institute of Physiology and Allied Sciences-- -

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: rs2248727; hg19: chrM-9541; COSMIC: COSV104419768; COSMIC: COSV104419768; API