rs16968029

chr19-33378269-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001806.4(CEBPG):c.-96-875C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,072 control chromosomes in the GnomAD database, including 3,348 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 0.20 (3348 hom., cov: 32)
• Consequence: CEBPG NM_001806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEBPG	NM_001806.4	c.-96-875C>T		intron_variant		ENST00000284000.9
CEBPG	NM_001252296.2	c.-96-875C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEBPG	ENST00000284000.9	c.-96-875C>T		intron_variant		1	NM_001806.4	P1
CEBPG	ENST00000585933.2	c.-96-875C>T		intron_variant		2		P1
CEBPG	ENST00000652630.1	c.-96-875C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31040 AN: 151954 Hom.: 3350 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.204

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.204 AC: 31044 AN: 152072 Hom.: 3348 Cov.: 32 AF XY: 0.201 AC XY: 14940 AN XY: 74330

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.202

Alfa AF: 0.219 Hom.: 931

Bravo AF: 0.201

Asia WGS AF: 0.161 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.063
Dann	Benign	0.71

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: rs16968029; hg19: chr19-33869175;