rs10513137

chr3-141424588-G-Achr3-141424588-G-C

Variant summary

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

The NM_001376113.1(ZBTB38):c.1-17801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,096 control chromosomes in the GnomAD database, including 2,856 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 0.16 (2856 hom., cov: 33)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB38	NM_001376113.1	c.1-17801G>A		intron_variant		ENST00000321464.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB38	ENST00000321464.7	c.1-17801G>A		intron_variant			NM_001376113.1	P1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24344 AN: 151978 Hom.: 2832 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0840

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.160 AC: 24400 AN: 152096 Hom.: 2856 Cov.: 33 AF XY: 0.161 AC XY: 11948 AN XY: 74362

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.0759

Gnomad4 NFE AF: 0.0839

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0902 Hom.: 1177

Bravo AF: 0.170

Asia WGS AF: 0.140 AC: 486 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.056
Dann	Benign	0.70

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: rs10513137; hg19: chr3-141143430;