M-13020-T-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Mitomap GenBank:
𝑓 0.00010 ( AC: 8 )
Consequence
ND5
synonymous
synonymous
Scores
Clinical Significance
Not reported in ClinVar
No linked disesase in Mitomap
Conservation
PhyloP100: -11.5
Genes affected
ND5 (HGNC:7461): (mitochondrially encoded NADH dehydrogenase 5) 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; Leigh disease; and MELAS syndrome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomadMitoHomoplasmic at 10
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ND5 | unassigned_transcript_4815 | c.684T>A | p.Gly228Gly | synonymous_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|
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:
8
Gnomad homoplasmic
AF:
AC:
10
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