chr10-3112981-C-T

Variant names:

• chr10-3112981-C-T
• rs7896691
• NM_002627.5:c.1155-138C>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.1155-138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 747,286 control chromosomes in the GnomAD database, including 296,580 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 0.85 (55384 hom., cov: 36)
  • Exomes 𝑓: 0.90 (241196 hom.)
• Consequence: PFKP NM_002627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PFKP	NM_002627.5	c.1155-138C>T		intron_variant	Intron 11 of 21	ENST00000381125.9	NP_002618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PFKP	ENST00000381125.9	c.1155-138C>T		intron_variant	Intron 11 of 21	1	NM_002627.5	ENSP00000370517.4

Frequencies

GnomAD3 genomes AF: 0.848 AC: 129097 AN: 152158 Hom.: 55362 Cov.: 36

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.871

GnomAD4 exome AF: 0.899 AC: 535064 AN: 595010 Hom.: 241196 AF XY: 0.902 AC XY: 279830 AN XY: 310064

African (AFR) AF: 0.709 AC: 11346 AN: 16002

American (AMR) AF: 0.890 AC: 25411 AN: 28544

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 15262 AN: 16696

East Asian (EAS) AF: 0.993 AC: 31742 AN: 31958

South Asian (SAS) AF: 0.936 AC: 50773 AN: 54268

European-Finnish (FIN) AF: 0.896 AC: 29376 AN: 32792

Middle Eastern (MID) AF: 0.923 AC: 3499 AN: 3790

European-Non Finnish (NFE) AF: 0.895 AC: 339745 AN: 379686

Other (OTH) AF: 0.892 AC: 27910 AN: 31274

GnomAD4 genome AF: 0.848 AC: 129168 AN: 152276 Hom.: 55384 Cov.: 36 AF XY: 0.849 AC XY: 63205 AN XY: 74440

African (AFR) AF: 0.709 AC: 29450 AN: 41538

American (AMR) AF: 0.871 AC: 13326 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3163 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5110 AN: 5178

South Asian (SAS) AF: 0.940 AC: 4540 AN: 4832

European-Finnish (FIN) AF: 0.891 AC: 9448 AN: 10606

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61157 AN: 68026

Other (OTH) AF: 0.872 AC: 1843 AN: 2114

Alfa AF: 0.877 Hom.: 94856

Bravo AF: 0.841

Asia WGS AF: 0.945 AC: 3287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		-0.61
PromoterAI		-0.0076	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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: rs7896691; hg19: chr10-3155173;