rs28608480
Positions:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP7BS2
The ENST00000361567.2(MT-ND5):āc.141T>Cā(p.Ser47=) 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 0.0050 ( AC: 307 )
Consequence
MT-ND5
ENST00000361567.2 synonymous
ENST00000361567.2 synonymous
Scores
Clinical Significance
Not reported in ClinVar
Possible-HCM-susceptibility
Conservation
PhyloP100: 0.166
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP7
Synonymous conserved (PhyloP=0.166 with no splicing effect.
BS2
High AC in GnomadMitoHomoplasmic at 303
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-ND5 | ENST00000361567.2 | c.141T>C | p.Ser47= | synonymous_variant | 1/1 | ENSP00000354813 | 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:
307
Gnomad homoplasmic
AF:
AC:
303
AN:
56418
Gnomad heteroplasmic
AF:
AC:
7
AN:
56418
Alfa
AF:
Hom.:
Mitomap
Possible-HCM-susceptibility
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at