rs10085637
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002612.4(PDK4):c.-208A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 508,604 control chromosomes in the GnomAD database, including 38,913 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 0.40 ( 12980 hom., cov: 31)
Exomes 𝑓: 0.36 ( 25933 hom. )
Consequence
PDK4
NM_002612.4 5_prime_UTR
NM_002612.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.950
Genes affected
PDK4 (HGNC:8812): (pyruvate dehydrogenase kinase 4) This gene is a member of the PDK/BCKDK protein kinase family and encodes a mitochondrial protein with a histidine kinase domain. This protein is located in the matrix of the mitrochondria and inhibits the pyruvate dehydrogenase complex by phosphorylating one of its subunits, thereby contributing to the regulation of glucose metabolism. Expression of this gene is regulated by glucocorticoids, retinoic acid and insulin. [provided by RefSeq, Jul 2008]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDK4 | NM_002612.4 | c.-208A>G | 5_prime_UTR_variant | 1/11 | ENST00000005178.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDK4 | ENST00000005178.6 | c.-208A>G | 5_prime_UTR_variant | 1/11 | 1 | NM_002612.4 | P1 | ||
PDK4-AS1 | ENST00000665332.1 | n.37-16550T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.401 AC: 60748AN: 151406Hom.: 12966 Cov.: 31
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GnomAD4 exome AF: 0.363 AC: 129790AN: 357080Hom.: 25933 Cov.: 5 AF XY: 0.366 AC XY: 67949AN XY: 185512
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GnomAD4 genome ? AF: 0.401 AC: 60801AN: 151524Hom.: 12980 Cov.: 31 AF XY: 0.402 AC XY: 29767AN XY: 74030
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at