dbSNP rs17132175: PFKP:c.871-79G>C (chr10-3108622-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002627.5(PFKP):c.871-79G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 1,034,094 control chromosomes in the GnomAD database, including 4,902 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 0.095 ( 746 hom., cov: 33)

Exomes 𝑓: 0.092 ( 4156 hom. )

Consequence

PFKP
NM_002627.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.957

Publications

6 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:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PFKP	NM_002627.5 link	c.871-79G>C		intron_variant	Intron 8 of 21	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.871-79G>C		intron_variant	Intron 8 of 21	1	NM_002627.5	ENSP00000370517.4		Q01813-1

Frequencies

GnomAD3 genomes

AF:

0.0945

AC:

14368

AN:

152064

Hom.:

743

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0935

Gnomad ASJ

AF:

0.0755

Gnomad EAS

AF:

0.00750

Gnomad SAS

AF:

0.0430

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0974

Gnomad OTH

AF:

0.0840

GnomAD4 exome

AF:

0.0924

AC:

81451

AN:

881912

Hom.:

4156

AF XY:

0.0898

AC XY:

40912

AN XY:

455680

show subpopulations

African (AFR)

AF:

0.106

AC:

2328

AN:

21902

American (AMR)

AF:

0.0881

AC:

3425

AN:

38886

Ashkenazi Jewish (ASJ)

AF:

0.0715

AC:

1514

AN:

21182

East Asian (EAS)

AF:

0.00293

AC:

107

AN:

36546

South Asian (SAS)

AF:

0.0468

AC:

3413

AN:

72872

European-Finnish (FIN)

AF:

0.104

AC:

5371

AN:

51612

Middle Eastern (MID)

AF:

0.0436

AC:

200

AN:

4582

European-Non Finnish (NFE)

AF:

0.104

AC:

61548

AN:

593594

Other (OTH)

AF:

0.0870

AC:

3545

AN:

40736

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3475

6950

10426

13901

17376

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0945

AC:

14382

AN:

152182

Hom.:

746

Cov.:

AF XY:

0.0945

AC XY:

7029

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.107

AC:

4438

AN:

41506

American (AMR)

AF:

0.0935

AC:

1429

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0755

AC:

262

AN:

3470

East Asian (EAS)

AF:

0.00771

AC:

AN:

5188

South Asian (SAS)

AF:

0.0426

AC:

205

AN:

4814

European-Finnish (FIN)

AF:

0.108

AC:

1147

AN:

10606

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0974

AC:

6620

AN:

67994

Other (OTH)

AF:

0.0836

AC:

177

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

695

1389

2084

2778

3473

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0945

Hom.:

Bravo

AF:

0.0934

Asia WGS

AF:

0.0310

AC:

107

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.58

(source)

DANN

Benign

0.61

PhyloP100

-0.96

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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rs17132175

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