rs2239633

Variant names:

• chr14-23119848-G-A
• rs2239633
• ENST00000696121.1:n.261+148C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-23119848-G-A
• chr14-23119848-G-C
• chr14-23119848-G-T

Variant summary

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

The ENST00000696121.1(CEBPE):​n.261+148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,132 control chromosomes in the GnomAD database, including 12,389 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 0.39 (12389 hom., cov: 33)
• Consequence: CEBPE ENST00000696121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

CEBPE (HGNC:1836): (CCAAT enhancer binding protein epsilon) The protein encoded by this gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-delta. The encoded protein may be essential for terminal differentiation and functional maturation of committed granulocyte progenitor cells. Mutations in this gene have been associated with Specific Granule Deficiency, a rare congenital disorder. Multiple variants of this gene have been described, but the full-length nature of only one has been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEBPE	ENST00000696121.1	n.261+148C>T		intron_variant	Intron 1 of 2
CEBPE	ENST00000696122.1	n.-150C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58780 AN: 152016 Hom.: 12371 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.387 AC: 58834 AN: 152132 Hom.: 12389 Cov.: 33 AF XY: 0.386 AC XY: 28685 AN XY: 74356

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.377

Alfa AF: 0.450 Hom.: 35723

Bravo AF: 0.371

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.28
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2239633; hg19: chr14-23589057;