10-3113348-A-G

Position:

• chr10-3113348-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002627.5(PFKP):​c.1225-24A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 1,573,858 control chromosomes in the GnomAD database, including 625,647 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 0.84 (54948 hom., cov: 36)
  • Exomes 𝑓: 0.90 (570699 hom.)
• Consequence: PFKP NM_002627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

Genes affected

PFKP (HGNC:8878): (phosphofructokinase, platelet) This gene encodes a member of the phosphofructokinase A protein family. The encoded enzyme is the platelet-specific isoform of phosphofructokinase and plays a key role in glycolysis regulation. This gene may play a role in metabolic reprogramming in some cancers, including clear cell renal cell carcinomas, and cancer of the bladder, breast, and lung. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -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 = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PFKP	NM_002627.5	c.1225-24A>G		intron_variant		ENST00000381125.9	NP_002618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PFKP	ENST00000381125.9	c.1225-24A>G		intron_variant		1	NM_002627.5	ENSP00000370517	P1

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128486 AN: 152170 Hom.: 54933 Cov.: 36

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.866

GnomAD3 exomes AF: 0.893 AC: 202034 AN: 226332 Hom.: 90613 AF XY: 0.899 AC XY: 108814 AN XY: 121094

Gnomad AFR exome AF: 0.692

Gnomad AMR exome AF: 0.894

Gnomad ASJ exome AF: 0.919

Gnomad EAS exome AF: 0.986

Gnomad SAS exome AF: 0.936

Gnomad FIN exome AF: 0.890

Gnomad NFE exome AF: 0.895

Gnomad OTH exome AF: 0.889

GnomAD4 exome AF: 0.895 AC: 1272700 AN: 1421570 Hom.: 570699 Cov.: 40 AF XY: 0.898 AC XY: 629200 AN XY: 700924

Gnomad4 AFR exome AF: 0.691

Gnomad4 AMR exome AF: 0.893

Gnomad4 ASJ exome AF: 0.913

Gnomad4 EAS exome AF: 0.992

Gnomad4 SAS exome AF: 0.937

Gnomad4 FIN exome AF: 0.894

Gnomad4 NFE exome AF: 0.895

Gnomad4 OTH exome AF: 0.891

GnomAD4 genome AF: 0.844 AC: 128543 AN: 152288 Hom.: 54948 Cov.: 36 AF XY: 0.844 AC XY: 62882 AN XY: 74466

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.867

Alfa AF: 0.891 Hom.: 25264

Bravo AF: 0.836

Asia WGS AF: 0.943 AC: 3279 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	1.7
DANN	Benign	0.25

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

Publications

LitVar

Other links and lift over

dbSNP: rs4881085; hg19: chr10-3155540;