Genetic Variant CEBPG:n.*884A>G (chr19-33381504-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000652630.1(CEBPG):n.*884A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 167,018 control chromosomes in the GnomAD database, including 857 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.096 ( 769 hom., cov: 33)

Exomes 𝑓: 0.10 ( 88 hom. )

Consequence

CEBPG
ENST00000652630.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.569

Publications

17 publications found

Variant links:

Genes affected

CEBPG (HGNC:1837): (CCAAT enhancer binding protein gamma) The C/EBP family of transcription factors regulates viral and cellular CCAAT/enhancer element-mediated transcription. C/EBP proteins contain the bZIP region, which is characterized by two motifs in the C-terminal half of the protein: a basic region involved in DNA binding and a leucine zipper motif involved in dimerization. The C/EBP family consist of several related proteins, C/EBP alpha, C/EBP beta, C/EBP gamma, and C/EBP delta, that form homodimers and that form heterodimers with each other. CCAAT/enhancer binding protein gamma may cooperate with Fos to bind PRE-I enhancer elements. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Nov 2011]

CEBPG links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEBPG	NM_001806.4 link	c.*1812A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000284000.9	NP_001797.1	P53567
CEBPG	NM_001252296.2 link	c.*1812A>G		3_prime_UTR_variant	Exon 2 of 2		NP_001239225.1	P53567

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CEBPG	ENST00000652630.1 link	n.*884A>G	non_coding_transcript_exon_variant	Exon 3 of 3			ENSP00000499062.1	P53567
CEBPG	ENST00000284000.9 link	c.*1812A>G	3_prime_UTR_variant	Exon 2 of 2	1	NM_001806.4	ENSP00000284000.2	P53567
CEBPG	ENST00000652630.1 link	n.*884A>G	3_prime_UTR_variant	Exon 3 of 3			ENSP00000499062.1	P53567
CEBPG	ENST00000585933.2 link	c.*1812A>G	3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000466022.2	P53567

Frequencies

GnomAD3 genomes

AF:

0.0957

AC:

14554

AN:

152104

Hom.:

769

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0848

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.0731

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.0173

Gnomad SAS

AF:

0.0585

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.0923

GnomAD4 exome

AF:

0.100

AC:

1483

AN:

14796

Hom.:

Cov.:

AF XY:

0.0981

AC XY:

690

AN XY:

7034

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.100

AC:

1458

AN:

14580

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.115

AC:

AN:

104

Other (OTH)

AF:

0.144

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

116

174

232

290

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0956

AC:

14558

AN:

152222

Hom.:

769

Cov.:

AF XY:

0.0940

AC XY:

6998

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0847

AC:

3518

AN:

41538

American (AMR)

AF:

0.0730

AC:

1117

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

565

AN:

3470

East Asian (EAS)

AF:

0.0172

AC:

AN:

5188

South Asian (SAS)

AF:

0.0594

AC:

287

AN:

4830

European-Finnish (FIN)

AF:

0.104

AC:

1100

AN:

10598

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7590

AN:

67986

Other (OTH)

AF:

0.0914

AC:

193

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

661

1323

1984

2646

3307

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.106

Hom.:

2765

Bravo

AF:

0.0944

Asia WGS

AF:

0.0350

AC:

122

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.5

(source)

DANN

Benign

0.51

PhyloP100

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over