chr3-141377343-C-G

Variant names:

• chr3-141377343-C-G
• rs9821337
• NM_001376113.1:c.-234-4082C>G

Variant summary

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

The NM_001376113.1(ZBTB38):​c.-234-4082C>G 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 152,176 control chromosomes in the GnomAD database, including 7,959 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 (7959 hom., cov: 33)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	NM_001376113.1	MANE Select	c.-234-4082C>G		intron	N/A	NP_001363042.1	Q8NAP3
	ZBTB38	NM_001080412.3		c.-479-4082C>G		intron	N/A	NP_001073881.2	Q8NAP3
	ZBTB38	NM_001376112.1		c.-234-4082C>G		intron	N/A	NP_001363041.1	Q8NAP3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.-234-4082C>G		intron	N/A	ENSP00000372635.5	Q8NAP3
	ZBTB38	ENST00000509842.5	TSL:1	c.-479-4082C>G		intron	N/A	ENSP00000426931.1	D6RE69
	ZBTB38	ENST00000507657.1	TSL:1	n.391-4082C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47288 AN: 152058 Hom.: 7947 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.311 AC: 47330 AN: 152176 Hom.: 7959 Cov.: 33 AF XY: 0.303 AC XY: 22580 AN XY: 74418

African (AFR) AF: 0.353 AC: 14649 AN: 41498

American (AMR) AF: 0.197 AC: 3020 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3472

East Asian (EAS) AF: 0.00308 AC: 16 AN: 5188

South Asian (SAS) AF: 0.171 AC: 824 AN: 4828

European-Finnish (FIN) AF: 0.364 AC: 3852 AN: 10594

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22990 AN: 67988

Other (OTH) AF: 0.266 AC: 561 AN: 2106

Alfa AF: 0.329 Hom.: 1060

Bravo AF: 0.300

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.35
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9821337; hg19: chr3-141096185;