rs9822195

Positions:

• chr3-141377894-C-T

Variant summary

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

The NM_001376113.1(ZBTB38):​c.-234-3531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,066 control chromosomes in the GnomAD database, including 7,945 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 0.31 (7945 hom., cov: 32)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

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 = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB38	NM_001376113.1	c.-234-3531C>T		intron_variant		ENST00000321464.7	NP_001363042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000321464.7	c.-234-3531C>T		intron_variant			NM_001376113.1	ENSP00000372635	P1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47291 AN: 151946 Hom.: 7933 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.311 AC: 47332 AN: 152066 Hom.: 7945 Cov.: 32 AF XY: 0.304 AC XY: 22567 AN XY: 74330

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.267

Alfa AF: 0.315 Hom.: 13296

Bravo AF: 0.300

Asia WGS AF: 0.100 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9822195; hg19: chr3-141096736;