rs7894025

Variant names:

• chr10-6267439-G-A
• rs7894025
• ENST00000784397.1:n.103+6637C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-6267439-G-A
• chr10-6267439-G-C

Variant summary

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

The ENST00000784397.1(ENSG00000302099):​n.103+6637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,986 control chromosomes in the GnomAD database, including 23,961 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 0.55 (23961 hom., cov: 31)
• Consequence: ENSG00000302099 ENST00000784397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 5 publications found

Genes affected

ENSG00000302099 (HGNC:):

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PFKFB3	XM_047425341.1	c.1455+41074G>A		intron_variant	Intron 14 of 14		XP_047281297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302099	ENST00000784397.1	n.103+6637C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83754 AN: 151870 Hom.: 23961 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.551 AC: 83776 AN: 151986 Hom.: 23961 Cov.: 31 AF XY: 0.548 AC XY: 40711 AN XY: 74292

African (AFR) AF: 0.401 AC: 16618 AN: 41430

American (AMR) AF: 0.554 AC: 8466 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1987 AN: 3466

East Asian (EAS) AF: 0.395 AC: 2038 AN: 5164

South Asian (SAS) AF: 0.600 AC: 2885 AN: 4812

European-Finnish (FIN) AF: 0.545 AC: 5751 AN: 10560

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.648 AC: 44074 AN: 67964

Other (OTH) AF: 0.543 AC: 1145 AN: 2108

Alfa AF: 0.602 Hom.: 11163

Bravo AF: 0.541

Asia WGS AF: 0.511 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.8
DANN	Benign	0.74
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs7894025; hg19: chr10-6309402;