rs6763931

Positions:

• chr3-141383991-G-A
• chr3-141383991-G-T

Variant summary

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

The NM_001376113.1(ZBTB38):​c.-172+2504G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,120 control chromosomes in the GnomAD database, including 24,013 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 (24013 hom., cov: 33)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB38	NM_001376113.1	c.-172+2504G>A		intron_variant		ENST00000321464.7	NP_001363042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000321464.7	c.-172+2504G>A		intron_variant			NM_001376113.1	ENSP00000372635	P1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80779 AN: 152002 Hom.: 23962 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.532 AC: 80896 AN: 152120 Hom.: 24013 Cov.: 33 AF XY: 0.525 AC XY: 39023 AN XY: 74362

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.451

Alfa AF: 0.432 Hom.: 32598

Bravo AF: 0.541

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6763931; hg19: chr3-141102833;