Genetic Variant PFKP:n.1594C>T (chr10-3136689-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000381072.5(PFKP):n.1594C>T variant causes a non coding transcript exon 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
ENST00000381072.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.341

Publications

22 publications found

Variant links:

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]

PFKP links:

ENSG00000278419 (HGNC:):

ENSG00000278419 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	c.*110C>T		3_prime_UTR_variant	Exon 22 of 22	ENST00000381125.9	NP_002618.1	Q01813-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PFKP	ENST00000381125.9 link	c.*110C>T		3_prime_UTR_variant	Exon 22 of 22	1	NM_002627.5	ENSP00000370517.4		Q01813-1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33088

AN:

152056

Hom.:

4466

Cov.:

show subpopulations

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.:

AF XY:

0.302

AC XY:

157888

AN XY:

523314

show subpopulations

African (AFR)

AF:

0.0472

AC:

1194

AN:

25276

American (AMR)

AF:

0.170

AC:

5419

AN:

31888

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

5010

AN:

19638

East Asian (EAS)

AF:

0.216

AC:

6944

AN:

32116

South Asian (SAS)

AF:

0.300

AC:

19327

AN:

64378

European-Finnish (FIN)

AF:

0.243

AC:

9890

AN:

40718

Middle Eastern (MID)

AF:

0.222

AC:

837

AN:

3766

European-Non Finnish (NFE)

AF:

0.323

AC:

256607

AN:

793832

Other (OTH)

AF:

0.279

AC:

12783

AN:

45816

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

10250

20499

30749

40998

51248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8012

16024

24036

32048

40060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.217

AC:

33085

AN:

152172

Hom.:

4466

Cov.:

AF XY:

0.217

AC XY:

16109

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0556

AC:

2309

AN:

41532

American (AMR)

AF:

0.216

AC:

3304

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

867

AN:

3472

East Asian (EAS)

AF:

0.223

AC:

1155

AN:

5180

South Asian (SAS)

AF:

0.295

AC:

1423

AN:

4822

European-Finnish (FIN)

AF:

0.226

AC:

2384

AN:

10570

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20827

AN:

67998

Other (OTH)

AF:

0.224

AC:

473

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1273

2547

3820

5094

6367

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.271

Hom.:

9536

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

(source)

DANN

Benign

0.66

PhyloP100

-0.34

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over