rs11531570

Variant names:

• chr7-95584390-G-A
• rs11531570
• NM_002612.4:c.*1251C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-95584390-G-A
• chr7-95584390-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002612.4(PDK4):​c.*1251C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,618 control chromosomes in the GnomAD database, including 13,603 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 0.42 (13603 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PDK4 NM_002612.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 11 publications found

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]

PDK4-AS1 (HGNC:55767): (PDK4 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDK4	NM_002612.4	c.*1251C>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000005178.6	NP_002603.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDK4	ENST00000005178.6	c.*1251C>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_002612.4	ENSP00000005178.5

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63172 AN: 151492 Hom.: 13597 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.461

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.417 AC: 63207 AN: 151610 Hom.: 13603 Cov.: 32 AF XY: 0.421 AC XY: 31182 AN XY: 74062

African (AFR) AF: 0.374 AC: 15419 AN: 41224

American (AMR) AF: 0.396 AC: 6045 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3470

East Asian (EAS) AF: 0.829 AC: 4273 AN: 5152

South Asian (SAS) AF: 0.458 AC: 2203 AN: 4814

European-Finnish (FIN) AF: 0.401 AC: 4210 AN: 10488

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27931 AN: 67900

Other (OTH) AF: 0.464 AC: 974 AN: 2100

Alfa AF: 0.416 Hom.: 39732

Bravo AF: 0.413

Asia WGS AF: 0.624 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.082
DANN	Benign	0.23
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11531570; hg19: chr7-95213702;