NM_002627.5:c.1155-138C>G

Variant names:

• chr10-3112981-C-G
• rs7896691
• NM_002627.5:c.1155-138C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002627.5(PFKP):​c.1155-138C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 36)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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.1155-138C>G		intron	N/A	NP_002618.1	Q01813-1
	PFKP	NM_001410880.1		c.1155-138C>G		intron	N/A	NP_001397809.1	A0A8V8TMY4
	PFKP	NM_001242339.2		c.1131-138C>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.1155-138C>G		intron	N/A	ENSP00000370517.4	Q01813-1
	PFKP	ENST00000699222.1		c.1155-138C>G		intron	N/A	ENSP00000514216.1	A0A8V8TMY4
	PFKP	ENST00000963518.1		c.1284-138C>G		intron	N/A	ENSP00000633577.1

Frequencies

GnomAD3 genomes Cov.: 36

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 595426 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 310288

African (AFR) AF: 0.00 AC: 0 AN: 16032

American (AMR) AF: 0.00 AC: 0 AN: 28570

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16704

East Asian (EAS) AF: 0.00 AC: 0 AN: 31958

South Asian (SAS) AF: 0.00 AC: 0 AN: 54284

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32808

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3792

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 379980

Other (OTH) AF: 0.00 AC: 0 AN: 31298

GnomAD4 genome Cov.: 36

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.36
PhyloP100		-0.61
PromoterAI		0.019	Neutral

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;