19-33382529-T-G

Variant names:

• chr19-33382529-T-G
• rs2772
• ENST00000652630.1:n.*1909T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000652630.1(CEBPG):​n.*1909T>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 0.178 in 167,102 control chromosomes in the GnomAD database, including 3,341 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 0.17 (2916 hom., cov: 33)
  • Exomes 𝑓: 0.23 (425 hom.)
• Consequence: CEBPG ENST00000652630.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786
• Publications: 12 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652630.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEBPG	NM_001806.4	MANE Select	c.*2837T>G		3_prime_UTR	Exon 2 of 2	NP_001797.1
	CEBPG	NM_001252296.2		c.*2837T>G		3_prime_UTR	Exon 2 of 2	NP_001239225.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEBPG	ENST00000652630.1		n.*1909T>G		non_coding_transcript_exon	Exon 3 of 3	ENSP00000499062.1
	CEBPG	ENST00000284000.9	TSL:1 MANE Select	c.*2837T>G		3_prime_UTR	Exon 2 of 2	ENSP00000284000.2
	CEBPG	ENST00000652630.1		n.*1909T>G		3_prime_UTR	Exon 3 of 3	ENSP00000499062.1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26232 AN: 152096 Hom.: 2907 Cov.: 33

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0722

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.230 AC: 3427 AN: 14890 Hom.: 425 Cov.: 0 AF XY: 0.231 AC XY: 1634 AN XY: 7070

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.230 AC: 3384 AN: 14702

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.298 AC: 25 AN: 84

Other (OTH) AF: 0.200 AC: 18 AN: 90

GnomAD4 genome AF: 0.172 AC: 26251 AN: 152212 Hom.: 2916 Cov.: 33 AF XY: 0.172 AC XY: 12831 AN XY: 74410

African (AFR) AF: 0.0545 AC: 2263 AN: 41558

American (AMR) AF: 0.272 AC: 4154 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5186

South Asian (SAS) AF: 0.0733 AC: 354 AN: 4830

European-Finnish (FIN) AF: 0.230 AC: 2428 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15740 AN: 67990

Other (OTH) AF: 0.214 AC: 451 AN: 2110

Alfa AF: 0.211 Hom.: 7320

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	8.9
DANN	Benign	0.78
PhyloP100		0.79
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2772; hg19: chr19-33873435;