rs7894025

Positions:

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

Variant summary

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

The XM_047425341.1(PFKFB3):​c.1455+41074G>A 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: PFKFB3 XM_047425341.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

Genes affected

PFKFB3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PFKFB3	XM_047425341.1	c.1455+41074G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.543

Alfa AF: 0.597 Hom.: 6975

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7894025; hg19: chr10-6309402;