chr10-6246792-T-G

Position:

• chr10-6246792-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363545.2(PFKFB3):​c.1516-7386T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,204 control chromosomes in the GnomAD database, including 2,106 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 0.16 (2106 hom., cov: 31)
• Consequence: PFKFB3 NM_001363545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

Genes affected

PFKFB3 (HGNC:8874): (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3) The protein encoded by this gene belongs to a family of bifunctional proteins that are involved in both the synthesis and degradation of fructose-2,6-bisphosphate, a regulatory molecule that controls glycolysis in eukaryotes. The encoded protein has a 6-phosphofructo-2-kinase activity that catalyzes the synthesis of fructose-2,6-bisphosphate (F2,6BP), and a fructose-2,6-biphosphatase activity that catalyzes the degradation of F2,6BP. This protein is required for cell cycle progression and prevention of apoptosis. It functions as a regulator of cyclin-dependent kinase 1, linking glucose metabolism to cell proliferation and survival in tumor cells. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PFKFB3	NM_001363545.2	c.1516-7386T>G		intron_variant
PFKFB3	XM_047425341.1	c.1455+20427T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PFKFB3	ENST00000640683.1	c.1516-7386T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23755 AN: 152086 Hom.: 2106 Cov.: 31

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.161

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 23759 AN: 152204 Hom.: 2106 Cov.: 31 AF XY: 0.156 AC XY: 11594 AN XY: 74410

Gnomad4 AFR AF: 0.0816

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0869

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.162

Alfa AF: 0.184 Hom.: 1845

Bravo AF: 0.146

Asia WGS AF: 0.114 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7902155; hg19: chr10-6288755;