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GeneBe

rs370688668

chrM-9947-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2

The ENST00000362079.2(MT-CO3):c.741G>A(p.Val247=) 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 0.0087 ( AC: 532 )

Consequence

MT-CO3
ENST00000362079.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -9.24
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]
MT-TG (HGNC:7486): (mitochondrially encoded tRNA glycine)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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-9947-G-A is Benign according to our data. Variant chrM-9947-G-A is described in ClinVar as [Benign]. Clinvar id is 235536.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=-9.24 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
High frequency in mitomap database: 0.0087
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 482

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COX3COX3.1 use as main transcriptc.741G>A p.Val247= synonymous_variant 1/1
TRNGTRNG.1 use as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-CO3ENST00000362079.2 linkuse as main transcriptc.741G>A p.Val247= synonymous_variant 1/1 P1
MT-TGENST00000387429.1 linkuse as main transcript upstream_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:
0.0087
AC:
532
Gnomad homoplasmic
AF:
0.0085
AC:
482
AN:
56411
Gnomad heteroplasmic
AF:
0.000071
AC:
4
AN:
56411
Alfa
AF:
0.00502
Hom.:
22

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 testingCenter for Pediatric Genomic Medicine, Children's Mercy Hospital and ClinicsOct 13, 2014- -

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: rs370688668; hg19: chrM-9948; API