dbSNP rs78863672: HS3ST3A1:c.-791G>T (chr17-13601920-C-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_006042.3(HS3ST3A1):c.-791G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. 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 0.52 ( 1791 hom., cov: 0)

Exomes 𝑓: 0.011 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

HS3ST3A1
NM_006042.3 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0430

Publications

1 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006042.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS3ST3A1	NM_006042.3	MANE Select	c.-791G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 2	NP_006033.1	Q9Y663
	HS3ST3A1	NM_006042.3	MANE Select	c.-791G>T		5_prime_UTR	Exon 1 of 2	NP_006033.1	Q9Y663

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS3ST3A1	ENST00000284110.2	TSL:1 MANE Select	c.-791G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 2	ENSP00000284110.1	Q9Y663
	HS3ST3A1	ENST00000284110.2	TSL:1 MANE Select	c.-791G>T		5_prime_UTR	Exon 1 of 2	ENSP00000284110.1	Q9Y663

Frequencies

GnomAD3 genomes

AF:

0.518

AC:

16026

AN:

30916

Hom.:

1789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.552

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.497

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.450

GnomAD4 exome

AF:

0.0110

AC:

AN:

912

Hom.:

Cov.:

AF XY:

0.0117

AC XY:

AN XY:

684

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0113

AC:

AN:

798

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.518

AC:

16050

AN:

30956

Hom.:

1791

Cov.:

AF XY:

0.520

AC XY:

7701

AN XY:

14814

show subpopulations

African (AFR)

AF:

0.552

AC:

11722

AN:

21232

American (AMR)

AF:

0.447

AC:

977

AN:

2188

Ashkenazi Jewish (ASJ)

AF:

0.303

AC:

182

AN:

600

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.496

AC:

342

AN:

690

European-Finnish (FIN)

AF:

0.497

AC:

150

AN:

302

Middle Eastern (MID)

AF:

0.324

AC:

AN:

European-Non Finnish (NFE)

AF:

0.452

AC:

2417

AN:

5346

Other (OTH)

AF:

0.452

AC:

187

AN:

414

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

644

1287

1931

2574

3218

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0216

Hom.:

Bravo

AF:

0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

0.043

PromoterAI

-0.11

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over