rs6795197

Positions:

• chr3-141328230-C-A

Variant summary

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

The ENST00000507698.1(ENSG00000249417):​n.166+38071G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,994 control chromosomes in the GnomAD database, including 8,884 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 0.33 (8884 hom., cov: 32)
• Consequence: ENST00000507698.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945

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]

(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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB38	NM_001080412.3	c.-739+3774C>A		intron_variant			NP_001073881.2
ZBTB38	XM_047447849.1	c.-567+3774C>A		intron_variant			XP_047303805.1
ZBTB38	XM_047447855.1	c.-494+3774C>A		intron_variant			XP_047303811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000509842.5	c.-739+3774C>A		intron_variant		1		ENSP00000426931
	ENST00000507698.1	n.166+38071G>T		intron_variant, non_coding_transcript_variant		3
PXYLP1	ENST00000637579.1	c.*289+16474C>A		intron_variant, NMD_transcript_variant		5		ENSP00000490114

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49908 AN: 151876 Hom.: 8882 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.328 AC: 49925 AN: 151994 Hom.: 8884 Cov.: 32 AF XY: 0.323 AC XY: 23980 AN XY: 74290

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.00637

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.300

Alfa AF: 0.337 Hom.: 2485

Bravo AF: 0.315

Asia WGS AF: 0.127 AC: 442 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.94
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6795197; hg19: chr3-141047072;