Variant rs61744056 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006041.3(HS3ST3B1):c.633T>C(p.Pro211=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 149,386 control chromosomes in the GnomAD database, including 27,369 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 0.57 ( 27369 hom., cov: 25)

Exomes 𝑓: 0.70 ( 338642 hom. )

Failed GnomAD Quality Control

Consequence

HS3ST3B1
NM_006041.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95

Variant links:

Genes affected

HS3ST3B1 (HGNC:5198): (heparan sulfate-glucosamine 3-sulfotransferase 3B1) The protein encoded by this gene is a type II integral membrane protein that belongs to the 3-O-sulfotransferases family. These proteins catalyze the addition of sulfate groups at the 3-OH position of glucosamine in heparan sulfate. The substrate specificity of individual members of the family is based on prior modification of the heparan sulfate chain, thus allowing different members of the family to generate binding sites for different proteins on the same heparan sulfate chain. Following treatment with a histone deacetylase inhibitor, expression of this gene is activated in a pancreatic cell line. The increased expression results in promotion of the epithelial-mesenchymal transition. In addition, the modification catalyzed by this protein allows herpes simplex virus membrane fusion and penetration. A very closely related homolog with an almost identical sulfotransferase domain maps less than 1 Mb away. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

HS3ST3B1 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=-0.57).

BP7

Synonymous conserved (PhyloP=-1.95 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
HS3ST3B1	NM_006041.3 linkuse as main transcript	c.633T>C	p.Pro211=	synonymous_variant	2/2	ENST00000360954.3
HS3ST3B1	XM_017025479.3 linkuse as main transcript	c.72T>C	p.Pro24=	synonymous_variant	2/2
HS3ST3B1	NR_130138.2 linkuse as main transcript	n.1071T>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS3ST3B1	ENST00000360954.3 linkuse as main transcript	c.633T>C	p.Pro211=	synonymous_variant	2/2	1	NM_006041.3	P1
HS3ST3B1	ENST00000466596.5 linkuse as main transcript	c.633T>C	p.Pro211=	synonymous_variant, NMD_transcript_variant	2/3	2

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

84856

AN:

149274

Hom.:

27368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.252

Gnomad AMI

AF:

0.631

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.599

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.643

Gnomad FIN

AF:

0.741

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.727

Gnomad OTH

AF:

0.561

GnomAD3 exomes

AF:

0.503

AC:

91744

AN:

182240

Hom.:

34515

AF XY:

0.508

AC XY:

48848

AN XY:

96250

show subpopulations

Gnomad AFR exome

AF:

0.179

Gnomad AMR exome

AF:

0.313

Gnomad ASJ exome

AF:

0.267

Gnomad EAS exome

AF:

0.546

Gnomad SAS exome

AF:

0.394

Gnomad FIN exome

AF:

0.670

Gnomad NFE exome

AF:

0.632

Gnomad OTH exome

AF:

0.482

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.701

AC:

858872

AN:

1225270

Hom.:

338642

Cov.:

AF XY:

0.694

AC XY:

421318

AN XY:

606808

show subpopulations

Gnomad4 AFR exome

AF:

0.185

Gnomad4 AMR exome

AF:

0.348

Gnomad4 ASJ exome

AF:

0.513

Gnomad4 EAS exome

AF:

0.591

Gnomad4 SAS exome

AF:

0.598

Gnomad4 FIN exome

AF:

0.734

Gnomad4 NFE exome

AF:

0.750

Gnomad4 OTH exome

AF:

0.650

GnomAD4 genome

AF:

0.568

AC:

84862

AN:

149386

Hom.:

27369

Cov.:

AF XY:

0.568

AC XY:

41318

AN XY:

72750

show subpopulations

Gnomad4 AFR

AF:

0.252

Gnomad4 AMR

AF:

0.561

Gnomad4 ASJ

AF:

0.599

Gnomad4 EAS

AF:

0.595

Gnomad4 SAS

AF:

0.644

Gnomad4 FIN

AF:

0.741

Gnomad4 NFE

AF:

0.727

Gnomad4 OTH

AF:

0.562

Alfa

AF:

0.504

Hom.:

3270

Bravo

AF:

0.539

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

6.1

DANN

Benign

0.64

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