rs7894025

Variant names:

• chr10-6267439-G-A
• rs7894025
• XM_047425341.1:c.1455+41074G>A

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

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]

ENSG00000302099 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784397.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302099	ENST00000784397.1		n.103+6637C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7894025;

hg19: chr10-6309402;