10-3136689-C-T

Variant names:

• chr10-3136689-C-T
• rs1053000
• NM_002627.5:c.*110C>T

Variant summary

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

The NM_002627.5(PFKP):​c.*110C>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 0.29 in 1,209,600 control chromosomes in the GnomAD database, including 54,355 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 0.22 (4466 hom., cov: 34)
  • Exomes 𝑓: 0.30 (49889 hom.)
• Consequence: PFKP NM_002627.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

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]

ENSG00000278419 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PFKP	NM_002627.5	c.*110C>T		3_prime_UTR_variant	Exon 22 of 22	ENST00000381125.9	NP_002618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PFKP	ENST00000381125.9	c.*110C>T		3_prime_UTR_variant	Exon 22 of 22	1	NM_002627.5	ENSP00000370517.4

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33088 AN: 152056 Hom.: 4466 Cov.: 34

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.227

GnomAD4 exome AF: 0.301 AC: 318011 AN: 1057428 Hom.: 49889 Cov.: 13 AF XY: 0.302 AC XY: 157888 AN XY: 523314

Gnomad4 AFR exome AF: 0.0472

Gnomad4 AMR exome AF: 0.170

Gnomad4 ASJ exome AF: 0.255

Gnomad4 EAS exome AF: 0.216

Gnomad4 SAS exome AF: 0.300

Gnomad4 FIN exome AF: 0.243

Gnomad4 NFE exome AF: 0.323

Gnomad4 OTH exome AF: 0.279

GnomAD4 genome AF: 0.217 AC: 33085 AN: 152172 Hom.: 4466 Cov.: 34 AF XY: 0.217 AC XY: 16109 AN XY: 74396

Gnomad4 AFR AF: 0.0556

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.224

Alfa AF: 0.279 Hom.: 7753

Bravo AF: 0.207

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1053000; hg19: chr10-3178881;