chr19-33301332-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004364.5(CEBPA):c.*6G>A variant causes a 3 prime UTR 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 Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CEBPA
NM_004364.5 3_prime_UTR
NM_004364.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.105
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CEBPA | NM_004364.5 | c.*6G>A | 3_prime_UTR_variant | 1/1 | ENST00000498907.3 | NP_004355.2 | ||
| CEBPA | NM_001285829.2 | c.*6G>A | 3_prime_UTR_variant | 1/1 | NP_001272758.1 | |||
| CEBPA | NM_001287424.2 | c.*6G>A | 3_prime_UTR_variant | 1/1 | NP_001274353.1 | |||
| CEBPA | NM_001287435.2 | c.*6G>A | 3_prime_UTR_variant | 1/1 | NP_001274364.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CEBPA | ENST00000498907.3 | c.*6G>A | 3_prime_UTR_variant | 1/1 | NM_004364.5 | ENSP00000427514 | P1 | |||
| ENST00000587312.1 | n.54C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1434540Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 712948
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1434540
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
712948
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Acute myeloid leukemia Uncertain:1
| Uncertain significance, no assertion criteria provided | clinical testing | Nadeem Sheikh Lab, University of the Punjab | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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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
No publications associated with this variant yet.