rs9829470

Positions:

• chr3-141334848-T-G

Variant summary

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

The NM_001080412.3(ZBTB38):​c.-739+10392T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,116 control chromosomes in the GnomAD database, including 5,905 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 0.27 (5905 hom., cov: 32)
• Consequence: ZBTB38 NM_001080412.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558

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]

ENSG00000249417 (HGNC:):

PXYLP1 (HGNC:26303): (2-phosphoxylose phosphatase 1) Enables phosphatase activity. Involved in chondroitin sulfate proteoglycan biosynthetic process; glycosaminoglycan biosynthetic process; and positive regulation of heparan sulfate proteoglycan biosynthetic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB38	NM_001080412.3	c.-739+10392T>G		intron_variant			NP_001073881.2
ZBTB38	XM_047447849.1	c.-567+10392T>G		intron_variant			XP_047303805.1
ZBTB38	XM_047447855.1	c.-494+10392T>G		intron_variant			XP_047303811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000509842.5	c.-739+10392T>G		intron_variant		1		ENSP00000426931.1
ENSG00000249417	ENST00000507698.1	n.166+31453A>C		intron_variant		3
PXYLP1	ENST00000637579.1	n.*289+23092T>G		intron_variant		5		ENSP00000490114.1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40810 AN: 151998 Hom.: 5906 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.268 AC: 40822 AN: 152116 Hom.: 5905 Cov.: 32 AF XY: 0.265 AC XY: 19717 AN XY: 74370

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.234

Alfa AF: 0.262 Hom.: 1052

Bravo AF: 0.256

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9829470; hg19: chr3-141053690;