rs9743

chrM-9698-T-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP7 BA1

The ENST00000362079.2(MT-CO3):c.492T>C(p.Leu164=) 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 0.040 (AC: 2433)
• Consequence: MT-CO3 ENST00000362079.2 synonymous
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -16.0

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=-16 with no splicing effect.
• BA1: High frequency in mitomap database: 0.0398

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COX3	COX3.1	c.492T>C	p.Leu164=	synonymous_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-CO3	ENST00000362079.2	c.492T>C	p.Leu164=	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: 0.040 AC: 2433

Gnomad homoplasmic AF: 0.052 AC: 2953 AN: 56410

Gnomad heteroplasmic AF: 0.000018 AC: 1 AN: 56410

Alfa AF: 0.154 Hom.: 688

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9743; hg19: chrM-9699;