5-228163-CTT-CTTTTT
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004168.4(SDHA):c.622-15_622-13dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000661 in 151,204 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 26)
Consequence
SDHA
NM_004168.4 intron
NM_004168.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.708
Genes affected
SDHA (HGNC:10680): (succinate dehydrogenase complex flavoprotein subunit A) This gene encodes a major catalytic subunit of succinate-ubiquinone oxidoreductase, a complex of the mitochondrial respiratory chain. The complex is composed of four nuclear-encoded subunits and is localized in the mitochondrial inner membrane. Mutations in this gene have been associated with a form of mitochondrial respiratory chain deficiency known as Leigh Syndrome. A pseudogene has been identified on chromosome 3q29. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHA | NM_004168.4 | c.622-15_622-13dupTTT | intron_variant | ENST00000264932.11 | NP_004159.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDHA | ENST00000264932.11 | c.622-15_622-13dupTTT | intron_variant | 1 | NM_004168.4 | ENSP00000264932.6 | ||||
ENSG00000286001 | ENST00000651543.1 | n.622-15_622-13dupTTT | intron_variant | ENSP00000499215.1 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151204Hom.: 0 Cov.: 26
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GnomAD4 exome Cov.: 29
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GnomAD4 genome AF: 0.00000661 AC: 1AN: 151204Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 73798
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at