chr14-23116809-A-C

Variant names:

• chr14-23116809-A-C
• rs8015478
• ENST00000696121.1:n.*227T>G

Variant summary

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

The ENST00000696121.1(CEBPE):​n.*227T>G variant causes a downstream gene 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: CEBPE ENST00000696121.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-0.99).
• 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
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

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.674

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8015478; hg19: chr14-23586018;