rs55722931
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001805.4(CEBPE):c.747C>T(p.Arg249=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0167 in 1,614,098 control chromosomes in the GnomAD database, including 299 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.013 ( 24 hom., cov: 32)
Exomes 𝑓: 0.017 ( 275 hom. )
Consequence
CEBPE
NM_001805.4 synonymous
NM_001805.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.820
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 14-23117586-G-A is Benign according to our data. Variant chr14-23117586-G-A is described in ClinVar as [Benign]. Clinvar id is 461468.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-23117586-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.82 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0135 (2049/152334) while in subpopulation NFE AF= 0.0181 (1229/68026). AF 95% confidence interval is 0.0172. There are 24 homozygotes in gnomad4. There are 1051 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 24 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEBPE | NM_001805.4 | c.747C>T | p.Arg249= | synonymous_variant | 2/2 | ENST00000206513.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEBPE | ENST00000206513.6 | c.747C>T | p.Arg249= | synonymous_variant | 2/2 | 1 | NM_001805.4 | P1 | |
CEBPE | ENST00000696121.1 | n.716C>T | non_coding_transcript_exon_variant | 3/3 | |||||
CEBPE | ENST00000696122.1 | n.493C>T | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.0135 AC: 2049AN: 152216Hom.: 24 Cov.: 32
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GnomAD3 exomes AF: 0.0152 AC: 3825AN: 251238Hom.: 50 AF XY: 0.0158 AC XY: 2152AN XY: 135838
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GnomAD4 exome AF: 0.0171 AC: 24946AN: 1461764Hom.: 275 Cov.: 32 AF XY: 0.0171 AC XY: 12405AN XY: 727220
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GnomAD4 genome ? AF: 0.0135 AC: 2049AN: 152334Hom.: 24 Cov.: 32 AF XY: 0.0141 AC XY: 1051AN XY: 74496
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Specific granule deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
CEBPE-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at