rs117559033

Variant names:

• chr16-25933223-C-T
• rs117559033
• NM_006040.3:c.735-202389C>T

Variant summary

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

The NM_006040.3(HS3ST4):​c.735-202389C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0467 in 152,178 control chromosomes in the GnomAD database, including 218 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 0.047 (218 hom., cov: 33)
• Consequence: HS3ST4 NM_006040.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 2 publications found

Genes affected

HS3ST4 (HGNC:5200): (heparan sulfate-glucosamine 3-sulfotransferase 4) This gene encodes the enzyme heparan sulfate D-glucosaminyl 3-O-sulfotransferase 4. This enzyme generates 3-O-sulfated glucosaminyl residues in heparan sulfate. Cell surface heparan sulfate is used as a receptor by herpes simplex virus type 1 (HSV-1), and expression of this gene is thought to play a role in HSV-1 pathogenesis. [provided by RefSeq, Jul 2008]

ENSG00000285882 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HS3ST4	NM_006040.3	c.735-202389C>T		intron_variant	Intron 1 of 1	ENST00000331351.6	NP_006031.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HS3ST4	ENST00000331351.6	c.735-202389C>T		intron_variant	Intron 1 of 1	1	NM_006040.3	ENSP00000330606.5
HS3ST4	ENST00000475436.1	n.176+46302C>T		intron_variant	Intron 1 of 1	3
ENSG00000285882	ENST00000648941.1	n.374-107691C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 7110 AN: 152060 Hom.: 218 Cov.: 33

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0603

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0467 AC: 7111 AN: 152178 Hom.: 218 Cov.: 33 AF XY: 0.0465 AC XY: 3457 AN XY: 74400

African (AFR) AF: 0.0356 AC: 1477 AN: 41514

American (AMR) AF: 0.0423 AC: 645 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0599 AC: 289 AN: 4822

European-Finnish (FIN) AF: 0.0397 AC: 421 AN: 10598

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

European-Non Finnish (NFE) AF: 0.0572 AC: 3892 AN: 68014

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0451 Hom.: 93

Bravo AF: 0.0455

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.64
PhyloP100		-0.51
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: rs117559033; hg19: chr16-25944544;