rs6440006

Variant names:

• chr3-141423849-G-A
• rs6440006
• NM_001376113.1:c.1-18540G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-141423849-G-A
• chr3-141423849-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.1-18540G>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
• Publications: 28 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=-0.98).
• 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 rank	MANE	Protein	UniProt
ZBTB38	NM_001376113.1	c.1-18540G>A		intron_variant	Intron 5 of 5	ENST00000321464.7	NP_001363042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000321464.7	c.1-18540G>A		intron_variant	Intron 5 of 5	6	NM_001376113.1	ENSP00000372635.5

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

African (AFR) AF: 0.829 AC: 34409 AN: 41512

American (AMR) AF: 0.454 AC: 6936 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3466

East Asian (EAS) AF: 0.331 AC: 1714 AN: 5174

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4822

European-Finnish (FIN) AF: 0.441 AC: 4650 AN: 10536

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29850 AN: 67946

Other (OTH) AF: 0.466 AC: 984 AN: 2110

Alfa AF: 0.472 Hom.: 28241

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
PhyloP100		-1.3
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: rs6440006; hg19: chr3-141142691;