dbSNP rs36101103: CEBPG:n.*1908G>A (chr19-33382528-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2

The ENST00000652630.1(CEBPG):n.*1908G>A 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 0.0246 in 167,166 control chromosomes in the GnomAD database, including 70 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 0.024 ( 67 hom., cov: 33)

Exomes 𝑓: 0.030 ( 3 hom. )

Consequence

CEBPG
ENST00000652630.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.544

Publications

5 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.024 (3653/152272) while in subpopulation NFE AF = 0.0346 (2354/68026). AF 95% confidence interval is 0.0334. There are 67 homozygotes in GnomAd4. There are 1738 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 67 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEBPG	NM_001806.4 link	c.*2836G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000284000.9	NP_001797.1	P53567
CEBPG	NM_001252296.2 link	c.*2836G>A		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.*1908G>A	non_coding_transcript_exon_variant	Exon 3 of 3			ENSP00000499062.1	P53567
CEBPG	ENST00000284000.9 link	c.*2836G>A	3_prime_UTR_variant	Exon 2 of 2	1	NM_001806.4	ENSP00000284000.2	P53567
CEBPG	ENST00000652630.1 link	n.*1908G>A	3_prime_UTR_variant	Exon 3 of 3			ENSP00000499062.1	P53567
CEBPG	ENST00000585933.2 link	c.*2836G>A	3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000466022.2	P53567

Frequencies

GnomAD3 genomes

AF:

0.0240

AC:

3656

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00606

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.0155

Gnomad ASJ

AF:

0.0579

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0251

Gnomad FIN

AF:

0.0298

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0346

Gnomad OTH

AF:

0.0215

GnomAD4 exome

AF:

0.0305

AC:

454

AN:

14894

Hom.:

Cov.:

AF XY:

0.0296

AC XY:

209

AN XY:

7070

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0303

AC:

446

AN:

14704

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0814

AC:

AN:

Other (OTH)

AF:

0.0111

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

102

127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0240

AC:

3653

AN:

152272

Hom.:

Cov.:

AF XY:

0.0233

AC XY:

1738

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.00604

AC:

251

AN:

41548

American (AMR)

AF:

0.0155

AC:

237

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0579

AC:

201

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.0247

AC:

119

AN:

4826

European-Finnish (FIN)

AF:

0.0298

AC:

316

AN:

10602

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0346

AC:

2354

AN:

68026

Other (OTH)

AF:

0.0213

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

188

376

564

752

940

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0310

Hom.:

Bravo

AF:

0.0219

Asia WGS

AF:

0.00837

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

8.0

(source)

DANN

Benign

0.66

PhyloP100

0.54

Mutation Taster

=99/1

polymorphism

(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