3-141439370-G-T

Variant names:

• chr3-141439370-G-T
• rs7612543
• NM_001376113.1:c.1-3019G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001376113.1(ZBTB38):​c.1-3019G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,058 control chromosomes in the GnomAD database, including 18,211 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 0.48 (18211 hom., cov: 33)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 14 publications found

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]

ENSG00000288585 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376113.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	NM_001376113.1	MANE Select	c.1-3019G>T		intron	N/A	NP_001363042.1
	ZBTB38	NM_001080412.3		c.1-3019G>T		intron	N/A	NP_001073881.2
	ZBTB38	NM_001350099.2		c.-1+1005G>T		intron	N/A	NP_001337028.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.1-3019G>T		intron	N/A	ENSP00000372635.5
	ZBTB38	ENST00000509883.5	TSL:1	c.1-3019G>T		intron	N/A	ENSP00000424254.1
	ZBTB38	ENST00000509842.5	TSL:1	c.1-3019G>T		intron	N/A	ENSP00000426931.1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72159 AN: 151942 Hom.: 18185 Cov.: 33

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.475 AC: 72230 AN: 152058 Hom.: 18211 Cov.: 33 AF XY: 0.467 AC XY: 34690 AN XY: 74296

African (AFR) AF: 0.643 AC: 26670 AN: 41496

American (AMR) AF: 0.422 AC: 6445 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1390 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1105 AN: 5170

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4820

European-Finnish (FIN) AF: 0.389 AC: 4100 AN: 10542

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29584 AN: 67974

Other (OTH) AF: 0.437 AC: 922 AN: 2110

Alfa AF: 0.437 Hom.: 64991

Bravo AF: 0.484

Asia WGS AF: 0.279 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.23
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7612543; hg19: chr3-141158212;