rs193302927

chrM-10238-T-C

Variant summary

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

The ENST00000361227.2(MT-ND3):c.180T>C(p.Ile60=) 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 0.057 (AC: 3480)
• Consequence: MT-ND3 ENST00000361227.2 synonymous
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -2.56

Genes affected

MT-ND3 (HGNC:7458): (mitochondrially encoded NADH dehydrogenase 3) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Leigh disease; and Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP7: Synonymous conserved (PhyloP=-2.56 with no splicing effect.
• BA1: High frequency in mitomap database: 0.056900002

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-ND3	ENST00000361227.2	c.180T>C	p.Ile60=	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: 0.057 AC: 3480

Gnomad homoplasmic AF: 0.025 AC: 1401 AN: 56425

Gnomad heteroplasmic AF: 0.000035 AC: 2 AN: 56425

Alfa AF: 0.0402 Hom.: 1652

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: rs193302927; hg19: chrM-10239;