rs28380140

Positions:

• chrM-9377-A-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP7 BS1 BS2

The ENST00000362079.2(MT-CO3):​c.171A>G​(p.Trp57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Mitomap GenBank: 𝑓 0.0084 (AC: 511)
• Consequence: MT-CO3 ENST00000362079.2 synonymous
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: 1.61

Genes affected

COX3 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP7: Synonymous conserved (PhyloP=1.61 with no splicing effect.
• BS1: High frequency in mitomap database: 0.0084
• BS2: High AC in GnomadMitoHomoplasmic at 493

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COX3	COX3.1	c.171A>G	p.Trp57=	synonymous_variant	1/1		YP_003024032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-CO3	ENST00000362079.2	c.171A>G	p.Trp57=	synonymous_variant	1/1			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: 0.0084 AC: 511

Gnomad homoplasmic AF: 0.0087 AC: 493 AN: 56361

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56361

Alfa AF: 0.00352 Hom.: 131

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
MutationTaster	Benign	0.71	N

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs28380140; hg19: chrM-9378; COSMIC: COSV62293526; COSMIC: COSV62293526;