Variant chr17-13496299-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000284110.2(HS3ST3A1):c.1119T>A(p.Pro373=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 1,529,094 control chromosomes in the GnomAD database, including 91,013 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 ( 8532 hom., cov: 27)

Exomes 𝑓: 0.36 ( 82481 hom. )

Consequence

HS3ST3A1
ENST00000284110.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.454

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=-0.59).

BP7

Synonymous conserved (PhyloP=-0.454 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
HS3ST3A1	NM_006042.3 linkuse as main transcript	c.1119T>A	p.Pro373=	synonymous_variant	2/2	ENST00000284110.2	NP_006033.1
HS3ST3A1	XM_011524114.4 linkuse as main transcript	c.522T>A	p.Pro174=	synonymous_variant	3/3		XP_011522416.1
HS3ST3A1	XM_047437228.1 linkuse as main transcript	c.522T>A	p.Pro174=	synonymous_variant	2/2		XP_047293184.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS3ST3A1	ENST00000284110.2 linkuse as main transcript	c.1119T>A	p.Pro373=	synonymous_variant	2/2	1	NM_006042.3	ENSP00000284110	P1
HS3ST3A1	ENST00000578576.1 linkuse as main transcript	c.513T>A	p.Pro171=	synonymous_variant	2/2	3		ENSP00000462696

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

49246

AN:

148452

Hom.:

8521

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.491

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.530

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.352

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.330

GnomAD3 exomes

AF:

0.385

AC:

78269

AN:

203314

Hom.:

15618

AF XY:

0.387

AC XY:

42813

AN XY:

110748

show subpopulations

Gnomad AFR exome

AF:

0.208

Gnomad AMR exome

AF:

0.563

Gnomad ASJ exome

AF:

0.315

Gnomad EAS exome

AF:

0.512

Gnomad SAS exome

AF:

0.545

Gnomad FIN exome

AF:

0.269

Gnomad NFE exome

AF:

0.344

Gnomad OTH exome

AF:

0.360

GnomAD4 exome

AF:

0.363

AC:

501192

AN:

1380528

Hom.:

82481

Cov.:

AF XY:

0.365

AC XY:

250051

AN XY:

684314

show subpopulations

Gnomad4 AFR exome

AF:

0.203

Gnomad4 AMR exome

AF:

0.536

Gnomad4 ASJ exome

AF:

0.327

Gnomad4 EAS exome

AF:

0.518

Gnomad4 SAS exome

AF:

0.491

Gnomad4 FIN exome

AF:

0.270

Gnomad4 NFE exome

AF:

0.353

Gnomad4 OTH exome

AF:

0.368

GnomAD4 genome

AF:

0.332

AC:

49294

AN:

148566

Hom.:

8532

Cov.:

AF XY:

0.338

AC XY:

24487

AN XY:

72342

show subpopulations

Gnomad4 AFR

AF:

0.211

Gnomad4 AMR

AF:

0.492

Gnomad4 ASJ

AF:

0.331

Gnomad4 EAS

AF:

0.531

Gnomad4 SAS

AF:

0.550

Gnomad4 FIN

AF:

0.283

Gnomad4 NFE

AF:

0.348

Gnomad4 OTH

AF:

0.333

Alfa

AF:

0.229

Hom.:

683

Bravo

AF:

0.347

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

1.1

DANN

Benign

0.78

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