3-141383991-G-A

Variant names:

• chr3-141383991-G-A
• rs6763931
• NM_001376113.1:c.-172+2504G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 137 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	NM_001376113.1	MANE Select	c.-172+2504G>A		intron	N/A	NP_001363042.1
	ZBTB38	NM_001080412.3		c.-417+2504G>A		intron	N/A	NP_001073881.2
	ZBTB38	NM_001376112.1		c.-172+2504G>A		intron	N/A	NP_001363041.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.-172+2504G>A		intron	N/A	ENSP00000372635.5
	ZBTB38	ENST00000509842.5	TSL:1	c.-417+2504G>A		intron	N/A	ENSP00000426931.1
	ZBTB38	ENST00000507657.1	TSL:1	n.453+2504G>A		intron	N/A

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

African (AFR) AF: 0.816 AC: 33882 AN: 41516

American (AMR) AF: 0.439 AC: 6706 AN: 15278

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

East Asian (EAS) AF: 0.327 AC: 1695 AN: 5176

South Asian (SAS) AF: 0.308 AC: 1486 AN: 4824

European-Finnish (FIN) AF: 0.442 AC: 4674 AN: 10572

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29734 AN: 67968

Other (OTH) AF: 0.451 AC: 952 AN: 2112

Alfa AF: 0.453 Hom.: 78405

Bravo AF: 0.541

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.50
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs6763931; hg19: chr3-141102833;