rs2853487

Positions:

Variant summary

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

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

Scores

Clinical Significance

Not reported in ClinVar
No linked disesase in Mitomap

Conservation

PhyloP100: -3.89
Variant links:
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]

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ACMG classification

Classification made for transcript

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-ND4LENST00000361335.1 linkuse as main transcriptc.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

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.

Other links and lift over

dbSNP: rs2853487; hg19: chrM-10590; API