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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002627.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PFKP	NM_002627.5	MANE Select	c.871-79G>C	intron	N/A	NP_002618.1
PFKP	NM_001410880.1		c.871-79G>C	intron	N/A	NP_001397809.1
PFKP	NM_001242339.2		c.847-79G>C	intron	N/A	NP_001229268.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PFKP	ENST00000381125.9	TSL:1 MANE Select	c.871-79G>C	intron	N/A	ENSP00000370517.4
PFKP	ENST00000699222.1		c.871-79G>C	intron	N/A	ENSP00000514216.1
PFKP	ENST00000381075.7	TSL:2	c.757-79G>C	intron	N/A	ENSP00000370465.3

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

Age Distribution

Exome Het

Exome Hom

Variant carriers

1678

3356

5034

6712

8390

<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:

0.0945

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

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<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:

0.0945

Hom.:

Bravo

AF:

0.0934

Asia WGS

AF:

0.0310

AC:

107

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over