rs10513137

Variant names:

• chr3-141424588-G-A
• rs10513137
• NM_001376113.1:c.1-17801G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-141424588-G-A
• chr3-141424588-G-C
• chr3-141424588-G-T

Variant summary

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

The NM_001376113.1(ZBTB38):​c.1-17801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,096 control chromosomes in the GnomAD database, including 2,856 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 0.16 (2856 hom., cov: 33)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 24 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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.1-17801G>A		intron	N/A	NP_001363042.1
	ZBTB38	NM_001080412.3		c.1-17801G>A		intron	N/A	NP_001073881.2
	ZBTB38	NM_001350099.2		c.-190-7564G>A		intron	N/A	NP_001337028.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.1-17801G>A		intron	N/A	ENSP00000372635.5
	ZBTB38	ENST00000509883.5	TSL:1	c.1-17801G>A		intron	N/A	ENSP00000424254.1
	ZBTB38	ENST00000509842.5	TSL:1	c.1-17801G>A		intron	N/A	ENSP00000426931.1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24344 AN: 151978 Hom.: 2832 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0840

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.160 AC: 24400 AN: 152096 Hom.: 2856 Cov.: 33 AF XY: 0.161 AC XY: 11948 AN XY: 74362

African (AFR) AF: 0.325 AC: 13445 AN: 41426

American (AMR) AF: 0.147 AC: 2240 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1235 AN: 5178

South Asian (SAS) AF: 0.0944 AC: 455 AN: 4822

European-Finnish (FIN) AF: 0.0759 AC: 803 AN: 10584

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0839 AC: 5710 AN: 68022

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.105 Hom.: 3999

Bravo AF: 0.170

Asia WGS AF: 0.140 AC: 486 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.056
DANN	Benign	0.70
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10513137; hg19: chr3-141143430;