14-23116809-A-C

Variant names:

• chr14-23116809-A-C
• rs8015478
• ENST00000733532.1:n.234+1391A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000733532.1(ENSG00000295888):​n.234+1391A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,904 control chromosomes in the GnomAD database, including 35,831 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 0.68 (35831 hom., cov: 30)
• Consequence: ENSG00000295888 ENST00000733532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 7 publications found

Genes affected

ENSG00000295888 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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
ENSG00000295888	ENST00000733532.1	n.234+1391A>C		intron_variant	Intron 1 of 1
CEBPE	ENST00000696121.1	n.*227T>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103861 AN: 151782 Hom.: 35804 Cov.: 30

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.684 AC: 103946 AN: 151904 Hom.: 35831 Cov.: 30 AF XY: 0.681 AC XY: 50587 AN XY: 74234

African (AFR) AF: 0.625 AC: 25861 AN: 41360

American (AMR) AF: 0.658 AC: 10056 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3466

East Asian (EAS) AF: 0.843 AC: 4357 AN: 5166

South Asian (SAS) AF: 0.588 AC: 2830 AN: 4814

European-Finnish (FIN) AF: 0.671 AC: 7075 AN: 10550

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49347 AN: 67954

Other (OTH) AF: 0.674 AC: 1420 AN: 2108

Alfa AF: 0.685 Hom.: 6671

Bravo AF: 0.681

Asia WGS AF: 0.702 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.56
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8015478; hg19: chr14-23586018;