rs6804032

chr3-114829624-C-T

Variant summary

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

The NM_001348800.3(ZBTB20):c.-416-28450G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,780 control chromosomes in the GnomAD database, including 1,579 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 0.13 (1579 hom., cov: 32)
• Consequence: ZBTB20 NM_001348800.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

Genes affected

ZBTB20 (HGNC:13503): (zinc finger and BTB domain containing 20) This gene, which was initially designated as dendritic cell-derived BTB/POZ zinc finger (DPZF), belongs to a family of transcription factors with an N-terminal BTB/POZ domain and a C-terminal DNA-bindng zinc finger domain. The BTB/POZ domain is a hydrophobic region of approximately 120 aa which mediates association with other BTB/POZ domain-containing proteins. This gene acts as a transcriptional repressor and plays a role in many processes including neurogenesis, glucose homeostasis, and postnatal growth. Mutations in this gene have been associated with Primrose syndrome as well as the 3q13.31 microdeletion syndrome. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB20	NM_001348800.3	c.-416-28450G>A		intron_variant		ENST00000675478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB20	ENST00000675478.1	c.-416-28450G>A		intron_variant			NM_001348800.3	A2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19445 AN: 151662 Hom.: 1580 Cov.: 32

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.0688

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.128 AC: 19437 AN: 151780 Hom.: 1579 Cov.: 32 AF XY: 0.130 AC XY: 9640 AN XY: 74182

Gnomad4 AFR AF: 0.0495

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0691

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.157

Alfa AF: 0.147 Hom.: 1058

Bravo AF: 0.117

Asia WGS AF: 0.0590 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.5
Dann	Benign	0.58

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: rs6804032; hg19: chr3-114548471;