rs878982719
Positions:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP7BS2
The ENST00000361390.2(MT-ND1):āc.192C>Gā(p.Ala64=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A64A) has been classified as Likely benign.
Frequency
Mitomap GenBank:
š 0.0020 ( AC: 125 )
Consequence
MT-ND1
ENST00000361390.2 synonymous
ENST00000361390.2 synonymous
Scores
Clinical Significance
Not reported in ClinVar
No linked disesase in Mitomap
Conservation
PhyloP100: -4.87
Genes affected
MT-ND1 (HGNC:7455): (mitochondrially encoded NADH dehydrogenase 1) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Located in mitochondrial membrane. Part of mitochondrial respiratory chain complex I. Implicated in several diseases, including MELAS syndrome; neurodegenerative disease (multiple); optic nerve disease (multiple); toxic shock syndrome; and type 2 diabetes mellitus. Biomarker of Alzheimer's disease; Parkinson's disease; and multiple sclerosis. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP7
Synonymous conserved (PhyloP=-4.87 with no splicing effect.
BS2
High AC in GnomadMitoHomoplasmic at 54
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-ND1 | ENST00000361390.2 | c.192C>G | p.Ala64= | synonymous_variant | 1/1 | ENSP00000354687 | 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:
125
Gnomad homoplasmic
AF:
AC:
54
AN:
56434
Gnomad heteroplasmic
AF:
AC:
0
AN:
56434
Alfa
AF:
Hom.:
Mitomap
No disease associated.
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at