M-12384-T-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP7BS2
The ENST00000361567.2(MT-ND5):āc.48T>Cā(p.Ile16=) 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.
Frequency
Mitomap GenBank:
š 0.00030 ( AC: 20 )
Consequence
MT-ND5
ENST00000361567.2 synonymous
ENST00000361567.2 synonymous
Scores
Clinical Significance
Not reported in ClinVar
No linked disesase in Mitomap
Conservation
PhyloP100: -14.2
Genes affected
MT-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]
MT-TL2 (HGNC:7491): (mitochondrially encoded tRNA leucine 2 (CUN))
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP7
Synonymous conserved (PhyloP=-14.2 with no splicing effect.
BS2
High AC in GnomadMitoHomoplasmic at 5
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRNL2 | TRNL2.1 use as main transcript | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-ND5 | ENST00000361567.2 | c.48T>C | p.Ile16= | synonymous_variant | 1/1 | P1 | |||
MT-TL2 | ENST00000387456.1 | 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:
20
Gnomad homoplasmic
AF:
AC:
5
AN:
56429
Gnomad heteroplasmic
AF:
AC:
3
AN:
56429
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