rs9825379

chr3-141418193-G-A

Variant summary

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

The NM_001376113.1(ZBTB38):c.-1+14162G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,952 control chromosomes in the GnomAD database, including 2,198 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 (2198 hom., cov: 32)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

Genes affected

ZBTB38 (HGNC:26636): (zinc finger and BTB domain containing 38) The protein encoded by this gene is a zinc finger transcriptional activator that binds methylated DNA. The encoded protein can form homodimers or heterodimers through the zinc finger domains. In mouse, inhibition of this protein has been associated with apoptosis in some cell types. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB38	NM_001376113.1	c.-1+14162G>A		intron_variant		ENST00000321464.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB38	ENST00000321464.7	c.-1+14162G>A		intron_variant			NM_001376113.1	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19808 AN: 151834 Hom.: 2192 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0420

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.131 AC: 19832 AN: 151952 Hom.: 2198 Cov.: 32 AF XY: 0.130 AC XY: 9634 AN XY: 74308

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.0636

Gnomad4 FIN AF: 0.0420

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0687 Hom.: 1256

Bravo AF: 0.140

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.46
Dann	Benign	0.51

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: rs9825379; hg19: chr3-141137035;