rs6602024

Variant names:

• chr10-3113045-A-G
• rs6602024
• NM_002627.5:c.1155-74A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-3113045-A-G
• chr10-3113045-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002627.5(PFKP):​c.1155-74A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 1,372,066 control chromosomes in the GnomAD database, including 547,945 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 0.86 (56423 hom., cov: 35)
  • Exomes 𝑓: 0.90 (491522 hom.)
• Consequence: PFKP NM_002627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 31 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PFKP	NM_002627.5	MANE Select	c.1155-74A>G		intron	N/A	NP_002618.1	Q01813-1
	PFKP	NM_001410880.1		c.1155-74A>G		intron	N/A	NP_001397809.1	A0A8V8TMY4
	PFKP	NM_001242339.2		c.1131-74A>G		intron	N/A	NP_001229268.1	Q01813-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PFKP	ENST00000381125.9	TSL:1 MANE Select	c.1155-74A>G		intron	N/A	ENSP00000370517.4	Q01813-1
	PFKP	ENST00000699222.1		c.1155-74A>G		intron	N/A	ENSP00000514216.1	A0A8V8TMY4
	PFKP	ENST00000963518.1		c.1284-74A>G		intron	N/A	ENSP00000633577.1

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130463 AN: 152114 Hom.: 56401 Cov.: 35

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.877

GnomAD4 exome AF: 0.897 AC: 1094408 AN: 1219834 Hom.: 491522 AF XY: 0.900 AC XY: 547415 AN XY: 608500

African (AFR) AF: 0.741 AC: 20983 AN: 28326

American (AMR) AF: 0.894 AC: 32869 AN: 36770

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 21934 AN: 23992

East Asian (EAS) AF: 0.993 AC: 35214 AN: 35476

South Asian (SAS) AF: 0.937 AC: 71811 AN: 76624

European-Finnish (FIN) AF: 0.893 AC: 39249 AN: 43940

Middle Eastern (MID) AF: 0.931 AC: 4963 AN: 5328

European-Non Finnish (NFE) AF: 0.895 AC: 820767 AN: 917324

Other (OTH) AF: 0.896 AC: 46618 AN: 52054

GnomAD4 genome AF: 0.857 AC: 130535 AN: 152232 Hom.: 56423 Cov.: 35 AF XY: 0.858 AC XY: 63859 AN XY: 74430

African (AFR) AF: 0.740 AC: 30744 AN: 41530

American (AMR) AF: 0.875 AC: 13384 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3161 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5103 AN: 5172

South Asian (SAS) AF: 0.940 AC: 4541 AN: 4830

European-Finnish (FIN) AF: 0.891 AC: 9452 AN: 10608

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61165 AN: 68010

Other (OTH) AF: 0.878 AC: 1853 AN: 2110

Alfa AF: 0.887 Hom.: 231256

Bravo AF: 0.851

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.33
PhyloP100		-1.0
PromoterAI		0.0011	Neutral
Mutation Taster		=6/94	disease causing

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

Other links and lift over

dbSNP: rs6602024; hg19: chr10-3155237;