chr7-95589126-T-C

Variant names:

• chr7-95589126-T-C
• rs12668651
• NM_002612.4:c.771+514A>G

Variant summary

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

The NM_002612.4(PDK4):​c.771+514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,112 control chromosomes in the GnomAD database, including 7,513 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 0.30 (7513 hom., cov: 32)
• Consequence: PDK4 NM_002612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDK4	NM_002612.4	c.771+514A>G		intron_variant	Intron 7 of 10	ENST00000005178.6	NP_002603.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDK4	ENST00000005178.6	c.771+514A>G		intron_variant	Intron 7 of 10	1	NM_002612.4	ENSP00000005178.5

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45117 AN: 151994 Hom.: 7498 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.330

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.297 AC: 45158 AN: 152112 Hom.: 7513 Cov.: 32 AF XY: 0.300 AC XY: 22338 AN XY: 74364

African (AFR) AF: 0.278 AC: 11539 AN: 41476

American (AMR) AF: 0.312 AC: 4772 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1438 AN: 3468

East Asian (EAS) AF: 0.782 AC: 4040 AN: 5168

South Asian (SAS) AF: 0.428 AC: 2059 AN: 4816

European-Finnish (FIN) AF: 0.175 AC: 1857 AN: 10600

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18477 AN: 67982

Other (OTH) AF: 0.334 AC: 705 AN: 2108

Alfa AF: 0.291 Hom.: 11357

Bravo AF: 0.304

Asia WGS AF: 0.580 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.4
DANN	Benign	0.75
PhyloP100		0.44
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: rs12668651; hg19: chr7-95218438;