10-3112981-C-T

Variant names:

• chr10-3112981-C-T
• rs7896691
• NM_002627.5:c.1155-138C>T

Variant summary

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

The NM_002627.5(PFKP):​c.1155-138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 747,286 control chromosomes in the GnomAD database, including 296,580 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 0.85 (55384 hom., cov: 36)
  • Exomes 𝑓: 0.90 (241196 hom.)
• Consequence: PFKP NM_002627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

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=-0.9).
• 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 rank	MANE	Protein	UniProt
PFKP	NM_002627.5	c.1155-138C>T		intron_variant	Intron 11 of 21	ENST00000381125.9	NP_002618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PFKP	ENST00000381125.9	c.1155-138C>T		intron_variant	Intron 11 of 21	1	NM_002627.5	ENSP00000370517.4

Frequencies

GnomAD3 genomes AF: 0.848 AC: 129097 AN: 152158 Hom.: 55362 Cov.: 36

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.871

GnomAD4 exome AF: 0.899 AC: 535064 AN: 595010 Hom.: 241196 AF XY: 0.902 AC XY: 279830 AN XY: 310064

Gnomad4 AFR exome AF: 0.709

Gnomad4 AMR exome AF: 0.890

Gnomad4 ASJ exome AF: 0.914

Gnomad4 EAS exome AF: 0.993

Gnomad4 SAS exome AF: 0.936

Gnomad4 FIN exome AF: 0.896

Gnomad4 NFE exome AF: 0.895

Gnomad4 OTH exome AF: 0.892

GnomAD4 genome AF: 0.848 AC: 129168 AN: 152276 Hom.: 55384 Cov.: 36 AF XY: 0.849 AC XY: 63205 AN XY: 74440

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.871

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: 0.872

Alfa AF: 0.866 Hom.: 7327

Bravo AF: 0.841

Asia WGS AF: 0.945 AC: 3287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.50

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: rs7896691; hg19: chr10-3155173;