chrM-4688-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2
The ENST00000361453.3(MT-ND2):āc.219T>Cā(p.Ala73=) 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 0.0067 ( AC: 410 )
Consequence
MT-ND2
ENST00000361453.3 synonymous
ENST00000361453.3 synonymous
Scores
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: -20.0
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 -11 ACMG points.
BP6
Variant M-4688-T-C is Benign according to our data. Variant chrM-4688-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 235516.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-20 with no splicing effect.
BS1
High frequency in mitomap database: 0.0067000003
BS2
High AC in GnomadMitoHomoplasmic at 325
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-ND2 | ENST00000361453.3 | c.219T>C | p.Ala73= | synonymous_variant | 1/1 | 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:
410
Gnomad homoplasmic
AF:
AC:
325
AN:
56412
Gnomad heteroplasmic
AF:
AC:
9
AN:
56412
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 | Aug 12, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at