3-141396377-T-C

Variant names:

• chr3-141396377-T-C
• rs1582874
• ENST00000509842.5:c.-232T>C

Variant summary

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

The ENST00000509842.5(ZBTB38):​c.-232T>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 0.526 in 154,892 control chromosomes in the GnomAD database, including 24,177 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 (23927 hom., cov: 32)
  • Exomes 𝑓: 0.41 (250 hom.)
• Consequence: ZBTB38 ENST00000509842.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 29 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB38	NM_001376113.1	c.-105-7550T>C		intron_variant	Intron 4 of 5	ENST00000321464.7	NP_001363042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000321464.7	c.-105-7550T>C		intron_variant	Intron 4 of 5	6	NM_001376113.1	ENSP00000372635.5

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80166 AN: 151994 Hom.: 23877 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.449

GnomAD4 exome AF: 0.405 AC: 1127 AN: 2780 Hom.: 250 Cov.: 0 AF XY: 0.388 AC XY: 720 AN XY: 1858

African (AFR) AF: 0.724 AC: 42 AN: 58

American (AMR) AF: 0.443 AC: 62 AN: 140

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 30 AN: 70

East Asian (EAS) AF: 0.170 AC: 33 AN: 194

South Asian (SAS) AF: 0.284 AC: 42 AN: 148

European-Finnish (FIN) AF: 0.466 AC: 27 AN: 58

Middle Eastern (MID) AF: 0.444 AC: 8 AN: 18

European-Non Finnish (NFE) AF: 0.420 AC: 827 AN: 1968

Other (OTH) AF: 0.444 AC: 56 AN: 126

GnomAD4 genome AF: 0.528 AC: 80282 AN: 152112 Hom.: 23927 Cov.: 32 AF XY: 0.519 AC XY: 38609 AN XY: 74360

African (AFR) AF: 0.822 AC: 34114 AN: 41526

American (AMR) AF: 0.428 AC: 6549 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1145 AN: 5186

South Asian (SAS) AF: 0.304 AC: 1465 AN: 4820

European-Finnish (FIN) AF: 0.437 AC: 4606 AN: 10546

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29688 AN: 67950

Other (OTH) AF: 0.449 AC: 950 AN: 2114

Alfa AF: 0.476 Hom.: 2239

Bravo AF: 0.537

Asia WGS AF: 0.290 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.15
DANN	Benign	0.31
PhyloP100		-1.7
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: rs1582874; hg19: chr3-141115219;