chr19-33301702-G-T

Variant names:

• chr19-33301702-G-T
• rs3745972
• NM_004364.5:c.713C>A

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_004364.5(CEBPA):​c.713C>A​(p.Ala238Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000000995 in 1,004,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A238V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000010 (0 hom.)
• Consequence: CEBPA NM_004364.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.10
• Publications: 3 publications found

Genes affected

CEBPA (HGNC:1833): (CCAAT enhancer binding protein alpha) This intronless gene encodes a transcription factor that contains a basic leucine zipper (bZIP) domain and recognizes the CCAAT motif in the promoters of target genes. The encoded protein functions in homodimers and also heterodimers with CCAAT/enhancer-binding proteins beta and gamma. Activity of this protein can modulate the expression of genes involved in cell cycle regulation as well as in body weight homeostasis. Mutation of this gene is associated with acute myeloid leukemia. The use of alternative in-frame non-AUG (GUG) and AUG start codons results in protein isoforms with different lengths. Differential translation initiation is mediated by an out-of-frame, upstream open reading frame which is located between the GUG and the first AUG start codons. [provided by RefSeq, Dec 2013]

ENSG00000267727 (HGNC:):

CEBPA-DT (HGNC:25710): (CEBPA divergent transcript)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.28093633).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEBPA	NM_004364.5	c.713C>A	p.Ala238Glu	missense_variant	Exon 1 of 1	ENST00000498907.3	NP_004355.2
CEBPA	NM_001287424.2	c.818C>A	p.Ala273Glu	missense_variant	Exon 1 of 1		NP_001274353.1
CEBPA	NM_001287435.2	c.671C>A	p.Ala224Glu	missense_variant	Exon 1 of 1		NP_001274364.1
CEBPA	NM_001285829.2	c.356C>A	p.Ala119Glu	missense_variant	Exon 1 of 1		NP_001272758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEBPA	ENST00000498907.3	c.713C>A	p.Ala238Glu	missense_variant	Exon 1 of 1	6	NM_004364.5	ENSP00000427514.1
ENSG00000267727	ENST00000587312.1	n.356+68G>T		intron_variant	Intron 1 of 1	3
CEBPA-DT	ENST00000718467.1	n.-52G>T		upstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 9.95e-7 AC: 1 AN: 1004724 Hom.: 0 Cov.: 30 AF XY: 0.00000210 AC XY: 1 AN XY: 475858

African (AFR) AF: 0.00 AC: 0 AN: 19990

American (AMR) AF: 0.00 AC: 0 AN: 5760

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10438

East Asian (EAS) AF: 0.00 AC: 0 AN: 17334

South Asian (SAS) AF: 0.00 AC: 0 AN: 19086

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16678

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3244

European-Non Finnish (NFE) AF: 0.00000114 AC: 1 AN: 874414

Other (OTH) AF: 0.00 AC: 0 AN: 37780

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Acute myeloid leukemia Uncertain:1

Apr 28, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces alanine with glutamic acid at codon 238 of the CEBPA protein (p.Ala238Glu). The alanine residue is moderately conserved and there is a moderate physicochemical difference between alanine and glutamic acid. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has not been reported in the literature in individuals with CEBPA-related conditions. ClinVar contains an entry for this variant (Variation ID: 21403). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	19
DANN	Benign	0.90
DEOGEN2	Benign	0.30	T
Eigen	Benign	-0.073
Eigen_PC	Benign	-0.053
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Benign	0.44	T
M_CAP	Pathogenic	0.38	D
MetaRNN	Benign	0.28	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.1	L
PhyloP100		5.1
PrimateAI	Pathogenic	0.91	D
PROVEAN	Benign	-0.61	N
REVEL	Benign	0.082
Sift	Benign	0.98	T
Sift4G	Benign	0.88	T
Polyphen		0.80	P
Vest4		0.37
MutPred		0.15		Gain of solvent accessibility (P = 0.0674);
MVP		0.36
ClinPred		0.31	T
GERP RS		4.1
Varity_R		0.16
gMVP		0.44
Mutation Taster		=72/28	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3745972; hg19: chr19-33792608;