rs9829470

Variant names:

• chr3-141334848-T-G
• rs9829470
• ENST00000509842.5:c.-739+10392T>G

Variant summary

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

The ENST00000509842.5(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 ENST00000509842.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 7 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]

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZBTB38	NM_001080412.3	c.-739+10392T>G		intron_variant	Intron 1 of 7		NP_001073881.2
ZBTB38	XM_047447849.1	c.-567+10392T>G		intron_variant	Intron 1 of 7		XP_047303805.1
ZBTB38	XM_047447855.1	c.-494+10392T>G		intron_variant	Intron 1 of 6		XP_047303811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000509842.5	c.-739+10392T>G		intron_variant	Intron 1 of 7	1		ENSP00000426931.1
ENSG00000249417	ENST00000507698.1	n.166+31453A>C		intron_variant	Intron 2 of 2	3
PXYLP1	ENST00000637579.1	n.*289+23092T>G		intron_variant	Intron 6 of 6	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

African (AFR) AF: 0.253 AC: 10481 AN: 41482

American (AMR) AF: 0.181 AC: 2761 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3472

East Asian (EAS) AF: 0.00482 AC: 25 AN: 5184

South Asian (SAS) AF: 0.183 AC: 881 AN: 4826

European-Finnish (FIN) AF: 0.369 AC: 3903 AN: 10570

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20973 AN: 67982

Other (OTH) AF: 0.234 AC: 492 AN: 2104

Alfa AF: 0.257 Hom.: 1170

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs9829470; hg19: chr3-141053690;