NM_004364.5:c.603G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_004364.5(CEBPA):c.603G>A(p.Leu201Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000677 in 147,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0000068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CEBPA
NM_004364.5 synonymous
NM_004364.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.02
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 19-33301812-C-T is Benign according to our data. Variant chr19-33301812-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 526826.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.02 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004364.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CEBPA | NM_004364.5 | MANE Select | c.603G>A | p.Leu201Leu | synonymous | Exon 1 of 1 | NP_004355.2 | ||
| CEBPA | NM_001287424.2 | c.708G>A | p.Leu236Leu | synonymous | Exon 1 of 1 | NP_001274353.1 | |||
| CEBPA | NM_001287435.2 | c.561G>A | p.Leu187Leu | synonymous | Exon 1 of 1 | NP_001274364.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CEBPA | ENST00000498907.3 | TSL:6 MANE Select | c.603G>A | p.Leu201Leu | synonymous | Exon 1 of 1 | ENSP00000427514.1 | ||
| ENSG00000267727 | ENST00000587312.1 | TSL:3 | n.357-3C>T | splice_region intron | N/A | ||||
| CEBPA-DT | ENST00000718467.1 | n.46+13C>T | intron | N/A |
Frequencies
GnomAD3 genomes 0.00000677 AC: 1AN: 147670Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
147670
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1100204Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 532838
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1100204
Hom.:
Cov.:
25
AF XY:
AC XY:
0
AN XY:
532838
African (AFR)
AF:
AC:
0
AN:
21718
American (AMR)
AF:
AC:
0
AN:
7912
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13144
East Asian (EAS)
AF:
AC:
0
AN:
23698
South Asian (SAS)
AF:
AC:
0
AN:
33800
European-Finnish (FIN)
AF:
AC:
0
AN:
23006
Middle Eastern (MID)
AF:
AC:
0
AN:
2840
European-Non Finnish (NFE)
AF:
AC:
0
AN:
931096
Other (OTH)
AF:
AC:
0
AN:
42990
GnomAD4 genome 0.00000677 AC: 1AN: 147670Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 71958 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
147670
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
71958
show subpopulations
African (AFR)
AF:
AC:
0
AN:
40772
American (AMR)
AF:
AC:
0
AN:
14918
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3390
East Asian (EAS)
AF:
AC:
0
AN:
5034
South Asian (SAS)
AF:
AC:
0
AN:
4778
European-Finnish (FIN)
AF:
AC:
0
AN:
9100
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
1
AN:
66424
Other (OTH)
AF:
AC:
0
AN:
2040
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
1
Acute myeloid leukemia (1)
-
-
1
Inborn genetic diseases (1)
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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