chrM-10489-A-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000361335.1(MT-ND4L):āc.20A>Gā(p.Asn7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Mitomap GenBank:
š 0.0 ( AC: 0 )
Consequence
MT-ND4L
ENST00000361335.1 missense
ENST00000361335.1 missense
Scores
Apogee2
Benign
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 1.40
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]
MT-TR (HGNC:7496): (mitochondrially encoded tRNA arginine)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very low frequency in mitomap database: 0.0
BP4
Apogee2 supports a benign effect, 0.07629886 < 0.5 .
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNR | TRNR.1 use as main transcript | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MT-ND4L | ENST00000361335.1 | c.20A>G | p.Asn7Ser | missense_variant | 1/1 | ENSP00000354728 | P1 | |||
MT-TR | ENST00000387439.1 | downstream_gene_variant |
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
0
Mitomap
No disease associated.
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leigh syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Oct 17, 2019 | The NC_012920.1:m.10489A>G (YP_003024034.1:p.Asn7Ser) variant in MTND4L gene is interpretated to be a Uncertain Significance variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: PP7, BP4 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
Hmtvar
Benign
AlphaMissense
Benign
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Uncertain
D
MutationTaster
Benign
N
PROVEAN
Pathogenic
D
Sift
Uncertain
D
Sift4G
Benign
T
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at