rs2239633

Positions:

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

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEBPE	ENST00000696121.1	n.261+148C>T		intron_variant, non_coding_transcript_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;