19-33382529-T-G

Position:

• chr19-33382529-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001806.4(CEBPG):​c.*2837T>G variant causes a 3 prime UTR 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 NM_001806.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEBPG	NM_001806.4	c.*2837T>G		3_prime_UTR_variant	2/2	ENST00000284000.9
CEBPG	NM_001252296.2	c.*2837T>G		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEBPG	ENST00000284000.9	c.*2837T>G		3_prime_UTR_variant	2/2	1	NM_001806.4	P1
CEBPG	ENST00000585933.2	c.*2837T>G		3_prime_UTR_variant	2/2	2		P1
CEBPG	ENST00000652630.1	c.*1909T>G		3_prime_UTR_variant, NMD_transcript_variant	3/3

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.230

Gnomad4 NFE exome AF: 0.298

Gnomad4 OTH exome AF: 0.200

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

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0733

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.214

Alfa AF: 0.212 Hom.: 4284

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	8.9
DANN	Benign	0.78

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

LitVar

Other links and lift over

dbSNP: rs2772; hg19: chr19-33873435;