14-23119848-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 80 publications found

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]

CEBPE Gene-Disease associations (from GenCC):

• specific granule deficiency 1

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• specific granule deficiency

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000295888 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000696121.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEBPE	ENST00000696121.1		n.261+148C>T		intron	N/A
	ENSG00000295888	ENST00000733532.1		n.234+4430G>A		intron	N/A
	CEBPE	ENST00000696122.1		n.-150C>T		upstream_gene	N/A

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

African (AFR) AF: 0.213 AC: 8861 AN: 41508

American (AMR) AF: 0.414 AC: 6335 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1871 AN: 5160

South Asian (SAS) AF: 0.374 AC: 1806 AN: 4828

European-Finnish (FIN) AF: 0.460 AC: 4868 AN: 10584

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32290 AN: 67968

Other (OTH) AF: 0.377 AC: 795 AN: 2110

Alfa AF: 0.440 Hom.: 70648

Bravo AF: 0.371

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.28
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2239633; hg19: chr14-23589057;