rs4791571

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006041.3(HS3ST3B1):​c.554+9687A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,932 control chromosomes in the GnomAD database, including 24,381 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 0.56 ( 24381 hom., cov: 31)

Consequence

HS3ST3B1
NM_006041.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0950
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HS3ST3B1NM_006041.3 linkuse as main transcriptc.554+9687A>G intron_variant ENST00000360954.3 NP_006032.1
HS3ST3B1NR_130138.2 linkuse as main transcriptn.992+9687A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HS3ST3B1ENST00000360954.3 linkuse as main transcriptc.554+9687A>G intron_variant 1 NM_006041.3 ENSP00000354213 P1
HS3ST3B1ENST00000466596.5 linkuse as main transcriptc.554+9687A>G intron_variant, NMD_transcript_variant 2 ENSP00000436078

Frequencies

GnomAD3 genomes
AF:
0.565
AC:
85712
AN:
151816
Hom.:
24359
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.533
Gnomad AMI
AF:
0.597
Gnomad AMR
AF:
0.578
Gnomad ASJ
AF:
0.668
Gnomad EAS
AF:
0.640
Gnomad SAS
AF:
0.629
Gnomad FIN
AF:
0.494
Gnomad MID
AF:
0.717
Gnomad NFE
AF:
0.574
Gnomad OTH
AF:
0.593
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.565
AC:
85780
AN:
151932
Hom.:
24381
Cov.:
31
AF XY:
0.563
AC XY:
41803
AN XY:
74242
show subpopulations
Gnomad4 AFR
AF:
0.533
Gnomad4 AMR
AF:
0.578
Gnomad4 ASJ
AF:
0.668
Gnomad4 EAS
AF:
0.640
Gnomad4 SAS
AF:
0.629
Gnomad4 FIN
AF:
0.494
Gnomad4 NFE
AF:
0.574
Gnomad4 OTH
AF:
0.595
Alfa
AF:
0.585
Hom.:
33482
Bravo
AF:
0.567
Asia WGS
AF:
0.600
AC:
2083
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
11
DANN
Benign
0.83

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.

Other links and lift over

dbSNP: rs4791571; hg19: chr17-14215076; COSMIC: COSV62906250; API