chr14-74889971-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001933.5(DLST):c.330+19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,610,318 control chromosomes in the GnomAD database, including 202 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0093 ( 17 hom., cov: 31)
Exomes 𝑓: 0.011 ( 185 hom. )
Consequence
DLST
NM_001933.5 intron
NM_001933.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.924
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 14-74889971-C-T is Benign according to our data. Variant chr14-74889971-C-T is described in ClinVar as [Benign]. Clinvar id is 2798137.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00934 (1420/152098) while in subpopulation SAS AF= 0.0407 (196/4820). AF 95% confidence interval is 0.036. There are 17 homozygotes in gnomad4. There are 720 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1408 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLST | NM_001933.5 | c.330+19C>T | intron_variant | ENST00000334220.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLST | ENST00000334220.9 | c.330+19C>T | intron_variant | 1 | NM_001933.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00926 AC: 1408AN: 151986Hom.: 16 Cov.: 31
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GnomAD3 exomes AF: 0.0121 AC: 3020AN: 249114Hom.: 47 AF XY: 0.0137 AC XY: 1841AN XY: 134684
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GnomAD4 exome AF: 0.0106 AC: 15422AN: 1458220Hom.: 185 Cov.: 29 AF XY: 0.0115 AC XY: 8374AN XY: 725458
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at