Variant rs28358278 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP7BA1

The ENST00000361227.2(MT-ND3):c.342C>T(p.Thr114=) 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 0.20 ( AC: 12419 )

Consequence

MT-ND3
ENST00000361227.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

No linked disesase in Mitomap

Conservation

PhyloP100: -8.49

Variant links:

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]

MT-ND3 links:

MT-TR (HGNC:7496): (mitochondrially encoded tRNA arginine)

MT-TR links:

TRNR (HGNC:):

TRNR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP7

Synonymous conserved (PhyloP=-8.49 with no splicing effect.

BA1

High frequency in mitomap database: 0.2031

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRNR	TRNR.1 use as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-ND3	ENST00000361227.2 linkuse as main transcript	c.342C>T	p.Thr114=	synonymous_variant	1/1			P1
MT-TR	ENST00000387439.1 linkuse as main transcript			upstream_gene_variant

Frequencies

GnomAD4 exome

Cov.:

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap GenBank

AF:

0.20

AC:

12419

Gnomad homoplasmic

AF:

0.053

AC:

2974

AN:

56379

Gnomad heteroplasmic

AF:

0.000018

AC:

AN:

56379

Alfa

AF:

0.0281

Hom.:

126

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

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.