chrM-10491-A-G

Position:

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The ENST00000361335.1(MT-ND4L):ā€‹c.22A>Gā€‹(p.Ile8Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I8T) has been classified as Uncertain significance.

Frequency

Mitomap GenBank:
š‘“ 0.0 ( AC: 0 )

Consequence

MT-ND4L
ENST00000361335.1 missense

Scores

Apogee2
Benign
0.020

Clinical Significance

not provided no classification provided O:1
No linked disesase in Mitomap

Conservation

PhyloP100: -0.914
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]
MT-TR (HGNC:7496): (mitochondrially encoded tRNA arginine)

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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, 0.01974126 < 0.5 .

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRNRTRNR.1 use as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MT-ND4LENST00000361335.1 linkuse as main transcriptc.22A>G p.Ile8Val missense_variant 1/1 ENSP00000354728 P1
MT-TRENST00000387439.1 linkuse as main transcript downstream_gene_variant

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0
AC:
0

Mitomap

No disease associated.

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

not provided Other:1
not provided, no classification providedphenotyping onlyGenomeConnect, ClinGen-Variant interpreted as Uncertain significance and reported on 10-08-2019 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
0.020
Hmtvar
Benign
0.13
AlphaMissense
Benign
0.073
BayesDel_addAF
Benign
-0.44
T
DEOGEN2
Benign
0.018
T
LIST_S2
Benign
0.82
T
MutationTaster
Benign
1.0
N
PROVEAN
Benign
-0.60
N
Sift
Benign
0.069
T
Sift4G
Benign
0.20
T
GERP RS
-9.8
Varity_R
0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrM-10492; API