XR_001738772.3:n.1486+32327A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_001738772.3(PDK1):​n.1486+32327A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,212 control chromosomes in the GnomAD database, including 44,935 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 0.76 ( 44935 hom., cov: 33)

Consequence

PDK1
XR_001738772.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44
Variant links:
Genes affected
PDK1 (HGNC:8809): (pyruvate dehydrogenase kinase 1) Pyruvate dehydrogenase (PDH) is a mitochondrial multienzyme complex that catalyzes the oxidative decarboxylation of pyruvate and is one of the major enzymes responsible for the regulation of homeostasis of carbohydrate fuels in mammals. The enzymatic activity is regulated by a phosphorylation/dephosphorylation cycle. Phosphorylation of PDH by a specific pyruvate dehydrogenase kinase (PDK) results in inactivation. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]

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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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PDK1XR_001738772.3 linkn.1486+32327A>G intron_variant Intron 12 of 13
PDK1XR_001738774.3 linkn.1426+32327A>G intron_variant Intron 11 of 11
PDK1XR_007076394.1 linkn.1486+32327A>G intron_variant Intron 12 of 13

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.760
AC:
115643
AN:
152094
Hom.:
44912
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.594
Gnomad AMI
AF:
0.715
Gnomad AMR
AF:
0.839
Gnomad ASJ
AF:
0.838
Gnomad EAS
AF:
0.980
Gnomad SAS
AF:
0.756
Gnomad FIN
AF:
0.850
Gnomad MID
AF:
0.737
Gnomad NFE
AF:
0.810
Gnomad OTH
AF:
0.775
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.760
AC:
115709
AN:
152212
Hom.:
44935
Cov.:
33
AF XY:
0.764
AC XY:
56879
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.594
Gnomad4 AMR
AF:
0.840
Gnomad4 ASJ
AF:
0.838
Gnomad4 EAS
AF:
0.980
Gnomad4 SAS
AF:
0.756
Gnomad4 FIN
AF:
0.850
Gnomad4 NFE
AF:
0.810
Gnomad4 OTH
AF:
0.774
Alfa
AF:
0.797
Hom.:
25732
Bravo
AF:
0.755
Asia WGS
AF:
0.840
AC:
2920
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.99
DANN
Benign
0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs836589; hg19: chr2-173493078; API