chr19-33301731-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004364.5(CEBPA):c.684G>A(p.Pro228Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000010 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CEBPA
NM_004364.5 synonymous
NM_004364.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.482
Publications
0 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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 19-33301731-C-T is Benign according to our data. Variant chr19-33301731-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 456699.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.482 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CEBPA | NM_004364.5 | c.684G>A | p.Pro228Pro | synonymous_variant | Exon 1 of 1 | ENST00000498907.3 | NP_004355.2 | |
| CEBPA | NM_001287424.2 | c.789G>A | p.Pro263Pro | synonymous_variant | Exon 1 of 1 | NP_001274353.1 | ||
| CEBPA | NM_001287435.2 | c.642G>A | p.Pro214Pro | synonymous_variant | Exon 1 of 1 | NP_001274364.1 | ||
| CEBPA | NM_001285829.2 | c.327G>A | p.Pro109Pro | synonymous_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.684G>A | p.Pro228Pro | synonymous_variant | Exon 1 of 1 | 6 | NM_004364.5 | ENSP00000427514.1 | ||
| ENSG00000267727 | ENST00000587312.1 | n.357-84C>T | intron_variant | Intron 1 of 1 | 3 | |||||
| CEBPA-DT | ENST00000718467.1 | n.-23C>T | upstream_gene_variant |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.95e-7 AC: 1AN: 1004602Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 475218 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1004602
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
475218
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
20000
American (AMR)
AF:
AC:
0
AN:
5892
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
10624
East Asian (EAS)
AF:
AC:
0
AN:
18748
South Asian (SAS)
AF:
AC:
0
AN:
19396
European-Finnish (FIN)
AF:
AC:
0
AN:
17186
Middle Eastern (MID)
AF:
AC:
0
AN:
2642
European-Non Finnish (NFE)
AF:
AC:
0
AN:
872336
Other (OTH)
AF:
AC:
0
AN:
37778
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Acute myeloid leukemia Benign:1
Jan 27, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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