rs878853062
Positions:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP6_ModerateBP7BS2
The ENST00000361453.3(MT-ND2):āc.354T>Cā(p.Val118=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Mitomap GenBank:
š 0.0048 ( AC: 292 )
Consequence
MT-ND2
ENST00000361453.3 synonymous
ENST00000361453.3 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -15.7
Genes affected
MT-ND2 (HGNC:7456): (mitochondrially encoded NADH dehydrogenase 2) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; multiple sclerosis; myocardial infarction; neurodegenerative disease (multiple); and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP6
Variant M-4823-T-C is Benign according to our data. Variant chrM-4823-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 235544.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-15.7 with no splicing effect.
BS2
High AC in GnomadMitoHomoplasmic at 685
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MT-ND2 | ENST00000361453.3 | c.354T>C | p.Val118= | synonymous_variant | 1/1 | ENSP00000355046 | P1 |
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:
292
Gnomad homoplasmic
AF:
AC:
685
AN:
56418
Gnomad heteroplasmic
AF:
AC:
6
AN:
56418
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jul 08, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at