16-22830171-T-G

Position:

• chr16-22830171-T-G

Variant summary

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

The NM_006043.2(HS3ST2):​c.485+15076T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 150,388 control chromosomes in the GnomAD database, including 1,325 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 0.13 (1325 hom., cov: 32)
• Consequence: HS3ST2 NM_006043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

Genes affected

HS3ST2 (HGNC:5195): (heparan sulfate-glucosamine 3-sulfotransferase 2) Heparan sulfate biosynthetic enzymes are key components in generating a myriad of distinct heparan sulfate fine structures that carry out multiple biologic activities. The enzyme encoded by this gene is a member of the heparan sulfate biosynthetic enzyme family. It is a type II integral membrane protein and possesses heparan sulfate glucosaminyl 3-O-sulfotransferase activity. This gene is expressed predominantly in brain and may play a role in the nervous system. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HS3ST2	NM_006043.2	c.485+15076T>G		intron_variant		ENST00000261374.4	NP_006034.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS3ST2	ENST00000261374.4	c.485+15076T>G		intron_variant		1	NM_006043.2	ENSP00000261374.3
HS3ST2	ENST00000473392.1	n.486-3105T>G		intron_variant		5		ENSP00000454505.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19263 AN: 150268 Hom.: 1318 Cov.: 32

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.0284

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.128 AC: 19298 AN: 150388 Hom.: 1325 Cov.: 32 AF XY: 0.131 AC XY: 9605 AN XY: 73502

Gnomad4 AFR AF: 0.0921

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.130

Alfa AF: 0.139 Hom.: 3450

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2283524; hg19: chr16-22841492;