19-33377107-A-G

Variant names:

• chr19-33377107-A-G
• rs1469084
• NM_001806.4:c.-96-2037A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001806.4(CEBPG):​c.-96-2037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,120 control chromosomes in the GnomAD database, including 27,369 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 0.59 (27369 hom., cov: 33)
• Consequence: CEBPG NM_001806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001806.4. 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.-96-2037A>G		intron	N/A	NP_001797.1
	CEBPG	NM_001252296.2		c.-96-2037A>G		intron	N/A	NP_001239225.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEBPG	ENST00000284000.9	TSL:1 MANE Select	c.-96-2037A>G		intron	N/A	ENSP00000284000.2
	CEBPG	ENST00000652630.1		n.-96-2037A>G		intron	N/A	ENSP00000499062.1
	CEBPG	ENST00000585933.2	TSL:2	c.-96-2037A>G		intron	N/A	ENSP00000466022.2

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90289 AN: 152002 Hom.: 27329 Cov.: 33

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.594 AC: 90385 AN: 152120 Hom.: 27369 Cov.: 33 AF XY: 0.592 AC XY: 44035 AN XY: 74360

African (AFR) AF: 0.719 AC: 29835 AN: 41496

American (AMR) AF: 0.557 AC: 8509 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2513 AN: 5184

South Asian (SAS) AF: 0.441 AC: 2126 AN: 4824

European-Finnish (FIN) AF: 0.572 AC: 6044 AN: 10574

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37654 AN: 67976

Other (OTH) AF: 0.600 AC: 1266 AN: 2110

Alfa AF: 0.561 Hom.: 53216

Bravo AF: 0.601

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.18
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: rs1469084; hg19: chr19-33868013;