rs731952
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000334220.9(DLST):c.902-179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,948 control chromosomes in the GnomAD database, including 7,721 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 7721 hom., cov: 31)
Consequence
DLST
ENST00000334220.9 intron
ENST00000334220.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.648
Genes affected
DLST (HGNC:2911): (dihydrolipoamide S-succinyltransferase) This gene encodes a mitochondrial protein that belongs to the 2-oxoacid dehydrogenase family. This protein is one of the three components (the E2 component) of the 2-oxoglutarate dehydrogenase complex that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLST | NM_001933.5 | c.902-179C>T | intron_variant | ENST00000334220.9 | NP_001924.2 | |||
DLST | XM_047431065.1 | c.353-179C>T | intron_variant | XP_047287021.1 | ||||
DLST | NR_033814.2 | n.882-179C>T | intron_variant, non_coding_transcript_variant | |||||
DLST | NR_045209.2 | n.891-179C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLST | ENST00000334220.9 | c.902-179C>T | intron_variant | 1 | NM_001933.5 | ENSP00000335304 | P1 | |||
DLST | ENST00000555089.5 | c.*531-179C>T | intron_variant, NMD_transcript_variant | 1 | ENSP00000452422 | |||||
DLST | ENST00000238671.11 | c.*640-179C>T | intron_variant, NMD_transcript_variant | 2 | ENSP00000238671 | |||||
DLST | ENST00000554612.5 | c.*645-179C>T | intron_variant, NMD_transcript_variant | 2 | ENSP00000451670 |
Frequencies
GnomAD3 genomes AF: 0.315 AC: 47867AN: 151830Hom.: 7712 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.315 AC: 47891AN: 151948Hom.: 7721 Cov.: 31 AF XY: 0.316 AC XY: 23489AN XY: 74262
GnomAD4 genome
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1034
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at