M-10499-A-G

Position:

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2

The ENST00000361335.1(MT-ND4L):ā€‹c.30A>Gā€‹(p.Leu10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (ā˜…).

Frequency

Mitomap GenBank:
š‘“ 0.0094 ( AC: 574 )

Consequence

MT-ND4L
ENST00000361335.1 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1
No linked disesase in Mitomap

Conservation

PhyloP100: -1.00
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 Benign. Variant got -11 ACMG points.

BP6
Variant M-10499-A-G is Benign according to our data. Variant chrM-10499-A-G is described in ClinVar as [Benign]. Clinvar id is 376866.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1 with no splicing effect.
BS1
High frequency in mitomap database: 0.0094
BS2
High AC in GnomadMitoHomoplasmic at 419

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.30A>G p.Leu10= synonymous_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:
0.0094
AC:
574
Gnomad homoplasmic
AF:
0.0074
AC:
419
AN:
56433
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56433
Alfa
AF:
0.00822
Hom.:
104

Mitomap

No disease associated.

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingCenter for Pediatric Genomic Medicine, Children's Mercy Hospital and ClinicsJan 26, 2017- -

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: rs1057520074; hg19: chrM-10500; API