dbSNP rs2072243: ENSG00000294706:n.43G>A (chr17-14301063-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000725301.1(ENSG00000294706):n.43G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 166,954 control chromosomes in the GnomAD database, including 3,757 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 0.20 ( 3377 hom., cov: 33)

Exomes 𝑓: 0.21 ( 380 hom. )

Consequence

ENSG00000294706
ENST00000725301.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539

Publications

4 publications found

Variant links:

COSMIC-nc: COSV62906239

Genes affected

ENSG00000294706 (HGNC:):

ENSG00000294706 links:

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HS3ST3B1	NM_006041.3 link	c.-456C>T		upstream_gene_variant		ENST00000360954.3	NP_006032.1	Q9Y662
HS3ST3B1	NR_130138.2 link	n.-18C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000294706	ENST00000725301.1 link	n.43G>A	non_coding_transcript_exon_variant	Exon 1 of 1
HS3ST3B1	ENST00000360954.3 link	c.-456C>T	upstream_gene_variant		1	NM_006041.3	ENSP00000354213.2	Q9Y662
HS3ST3B1	ENST00000466596.5 link	n.-456C>T	upstream_gene_variant		2		ENSP00000436078.1	Q9Y662

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30907

AN:

152132

Hom.:

3373

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.358

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.235

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.237

GnomAD4 exome

AF:

0.213

AC:

3138

AN:

14704

Hom.:

380

Cov.:

AF XY:

0.220

AC XY:

1650

AN XY:

7504

show subpopulations

African (AFR)

AF:

0.148

AC:

AN:

588

American (AMR)

AF:

0.238

AC:

AN:

336

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

150

AN:

570

East Asian (EAS)

AF:

0.253

AC:

174

AN:

688

South Asian (SAS)

AF:

0.227

AC:

107

AN:

472

European-Finnish (FIN)

AF:

0.117

AC:

AN:

540

Middle Eastern (MID)

AF:

0.378

AC:

AN:

European-Non Finnish (NFE)

AF:

0.216

AC:

2249

AN:

10434

Other (OTH)

AF:

0.200

AC:

200

AN:

1002

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

114

227

341

454

568

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.203

AC:

30926

AN:

152250

Hom.:

3377

Cov.:

AF XY:

0.200

AC XY:

14905

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.138

AC:

5721

AN:

41566

American (AMR)

AF:

0.217

AC:

3321

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.304

AC:

1056

AN:

3470

East Asian (EAS)

AF:

0.236

AC:

1216

AN:

5160

South Asian (SAS)

AF:

0.305

AC:

1469

AN:

4824

European-Finnish (FIN)

AF:

0.131

AC:

1388

AN:

10616

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.232

AC:

15808

AN:

67996

Other (OTH)

AF:

0.243

AC:

513

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1266

2533

3799

5066

6332

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

340

680

1020

1360

1700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.205

Hom.:

415

Bravo

AF:

0.208

Asia WGS

AF:

0.258

AC:

898

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.5

(source)

DANN

Benign

0.93

PhyloP100

-0.54

PromoterAI

0.044

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over