M-10589-G-A

Position:

• chrM-10589-G-A

Variant summary

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

The ENST00000361335.1(MT-ND4L):​c.120G>A​(p.Leu40=) 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 0.032 (AC: 1938)
• Consequence: MT-ND4L ENST00000361335.1 synonymous
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -3.89

Genes affected

MT-ND4L (HGNC:7460): (mitochondrially encoded NADH 4L dehydrogenase) Predicted to enable NADH dehydrogenase (ubiquinone) activity. Predicted to be located in mitochondrial inner membrane. Implicated in Leber hereditary optic neuropathy and diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP7: Synonymous conserved (PhyloP=-3.89 with no splicing effect.
• BA1: High frequency in mitomap database: 0.0317

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-ND4L	ENST00000361335.1	c.120G>A	p.Leu40=	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: 0.032 AC: 1938

Gnomad homoplasmic AF: 0.018 AC: 1039 AN: 56423

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56423

Alfa AF: 0.0119 Hom.: 444

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: rs2853487; hg19: chrM-10590;