dbSNP rs2072242: HS3ST3B1:c.-426T>A (chr17-14301093-T-A) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_006041.3(HS3ST3B1):c.-426T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

HS3ST3B1
NM_006041.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.578

Publications

6 publications found

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:

ENSG00000294706 (HGNC:):

ENSG00000294706 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.18).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HS3ST3B1	NM_006041.3 link	c.-426T>A		5_prime_UTR_variant	Exon 1 of 2	ENST00000360954.3	NP_006032.1	Q9Y662
HS3ST3B1	NR_130138.2 link	n.13T>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
HS3ST3B1	ENST00000360954.3 link	c.-426T>A	5_prime_UTR_variant	Exon 1 of 2	1	NM_006041.3	ENSP00000354213.2	Q9Y662
HS3ST3B1	ENST00000466596.5 link	n.-426T>A	non_coding_transcript_exon_variant	Exon 1 of 3	2		ENSP00000436078.1	Q9Y662
ENSG00000294706	ENST00000725301.1 link	n.13A>T	non_coding_transcript_exon_variant	Exon 1 of 1
HS3ST3B1	ENST00000466596.5 link	n.-426T>A	5_prime_UTR_variant	Exon 1 of 3	2		ENSP00000436078.1	Q9Y662

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

33098

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

16650

African (AFR)

AF:

0.00

AC:

AN:

1114

American (AMR)

AF:

0.00

AC:

AN:

768

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1256

East Asian (EAS)

AF:

0.00

AC:

AN:

1892

South Asian (SAS)

AF:

0.00

AC:

AN:

1200

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1430

Middle Eastern (MID)

AF:

0.00

AC:

AN:

176

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

22958

Other (OTH)

AF:

0.00

AC:

AN:

2304

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

12118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.18

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

0.58

PromoterAI

0.10

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over