3-141402972-A-C

Position:

• chr3-141402972-A-C

Variant summary

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

The ENST00000513570.1(ZBTB38):​c.-286A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,210 control chromosomes in the GnomAD database, including 24,289 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 0.53 (24279 hom., cov: 32)
  • Exomes 𝑓: 0.41 (10 hom.)
• Consequence: ZBTB38 ENST00000513570.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

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=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB38	NM_001376113.1	c.-105-955A>C		intron_variant		ENST00000321464.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB38	ENST00000321464.7	c.-105-955A>C		intron_variant			NM_001376113.1	P1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81141 AN: 151996 Hom.: 24231 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.452

GnomAD4 exome AF: 0.406 AC: 39 AN: 96 Hom.: 10 Cov.: 0 AF XY: 0.417 AC XY: 35 AN XY: 84

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.381

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.534 AC: 81254 AN: 152114 Hom.: 24279 Cov.: 32 AF XY: 0.527 AC XY: 39169 AN XY: 74360

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.453

Alfa AF: 0.434 Hom.: 16048

Bravo AF: 0.544

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	17
DANN	Benign	0.74

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: rs2871960; hg19: chr3-141121814;