19-33377107-A-G

Position:

• chr19-33377107-A-G

Variant summary

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

The ENST00000284000.9(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 ENST00000284000.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEBPG	NM_001806.4	c.-96-2037A>G		intron_variant		ENST00000284000.9	NP_001797.1
CEBPG	NM_001252296.2	c.-96-2037A>G		intron_variant			NP_001239225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEBPG	ENST00000284000.9	c.-96-2037A>G		intron_variant		1	NM_001806.4	ENSP00000284000	P1
CEBPG	ENST00000585933.2	c.-96-2037A>G		intron_variant		2		ENSP00000466022	P1
CEBPG	ENST00000652630.1	c.-96-2037A>G		intron_variant, NMD_transcript_variant				ENSP00000499062

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

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.600

Alfa AF: 0.557 Hom.: 35422

Bravo AF: 0.601

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.76

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: rs1469084; hg19: chr19-33868013;