rs6440006

Positions:

• chr3-141423849-G-A
• chr3-141423849-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.1-18540G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,042 control chromosomes in the GnomAD database, including 24,632 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 0.54 (24632 hom., cov: 33)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB38	NM_001376113.1	c.1-18540G>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.1-18540G>A		intron_variant			NM_001376113.1	ENSP00000372635	P1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81745 AN: 151924 Hom.: 24585 Cov.: 33

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.538 AC: 81855 AN: 152042 Hom.: 24632 Cov.: 33 AF XY: 0.531 AC XY: 39474 AN XY: 74330

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.466

Alfa AF: 0.470 Hom.: 4118

Bravo AF: 0.551

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.090
DANN	Benign	0.60

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: rs6440006; hg19: chr3-141142691;