Variant rs28663356 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006042.3(HS3ST3A1):c.39G>T(p.Ser13Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,591,590 control chromosomes in the GnomAD database, including 556 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 0.034 ( 241 hom., cov: 33)

Exomes 𝑓: 0.010 ( 315 hom. )

Consequence

HS3ST3A1
NM_006042.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

Variant links:

Genes affected

HS3ST3A1 (HGNC:5196): (heparan sulfate-glucosamine 3-sulfotransferase 3A1) 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. The sulfotransferase domain of this enzyme is highly similar to the same domain of heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3B1, and these two enzymes sulfate an identical disaccharide. This gene is widely expressed, with the most abundant expression in liver and placenta. [provided by RefSeq, Dec 2014]

HS3ST3A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP7

Synonymous conserved (PhyloP=-1.43 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.098 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HS3ST3A1	NM_006042.3 linkuse as main transcript	c.39G>T	p.Ser13Ser	synonymous_variant	1/2	ENST00000284110.2	NP_006033.1	Q9Y663
HS3ST3A1	XM_017025480.3 linkuse as main transcript	c.39G>T	p.Ser13Ser	synonymous_variant	1/2		XP_016880969.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS3ST3A1	ENST00000284110.2 linkuse as main transcript	c.39G>T	p.Ser13Ser	synonymous_variant	1/2	1	NM_006042.3	ENSP00000284110.1		Q9Y663

Frequencies

GnomAD3 genomes

AF:

0.0337

AC:

5122

AN:

152138

Hom.:

238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0175

Gnomad ASJ

AF:

0.0256

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.0294

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.00566

Gnomad OTH

AF:

0.0248

GnomAD3 exomes

AF:

0.0160

AC:

3341

AN:

208742

Hom.:

AF XY:

0.0161

AC XY:

1830

AN XY:

113348

show subpopulations

Gnomad AFR exome

AF:

0.104

Gnomad AMR exome

AF:

0.00857

Gnomad ASJ exome

AF:

0.0265

Gnomad EAS exome

AF:

0.0000662

Gnomad SAS exome

AF:

0.0348

Gnomad FIN exome

AF:

0.00157

Gnomad NFE exome

AF:

0.00642

Gnomad OTH exome

AF:

0.0125

GnomAD4 exome

AF:

0.0102

AC:

14744

AN:

1439344

Hom.:

315

Cov.:

AF XY:

0.0107

AC XY:

7614

AN XY:

714416

show subpopulations

Gnomad4 AFR exome

AF:

0.104

Gnomad4 AMR exome

AF:

0.00896

Gnomad4 ASJ exome

AF:

0.0239

Gnomad4 EAS exome

AF:

0.0000530

Gnomad4 SAS exome

AF:

0.0340

Gnomad4 FIN exome

AF:

0.00131

Gnomad4 NFE exome

AF:

0.00594

Gnomad4 OTH exome

AF:

0.0143

GnomAD4 genome

AF:

0.0337

AC:

5136

AN:

152246

Hom.:

241

Cov.:

AF XY:

0.0336

AC XY:

2500

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.0175

Gnomad4 ASJ

AF:

0.0256

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.0294

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00568

Gnomad4 OTH

AF:

0.0246

Alfa

AF:

0.0136

Hom.:

Bravo

AF:

0.0366

Asia WGS

AF:

0.0160

AC:

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.92

DANN

Benign

0.71

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over