chrM-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):āc.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
ENST00000361335.1 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -1.00
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 |
---|---|---|---|---|---|---|---|---|
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.30A>G | p.Leu10= | synonymous_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:
574
Gnomad homoplasmic
AF:
AC:
419
AN:
56433
Gnomad heteroplasmic
AF:
AC:
1
AN:
56433
Alfa
AF:
Hom.:
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 submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 26, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at