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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
HS3ST3A1	NM_006042.3 link	c.-791G>T	5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 2	ENST00000284110.2	NP_006033.1	Q9Y663
HS3ST3A1	NM_006042.3 link	c.-791G>T	5_prime_UTR_variant	Exon 1 of 2	ENST00000284110.2	NP_006033.1	Q9Y663
HS3ST3A1	XM_017025480.3 link	c.-791G>T	5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 2		XP_016880969.1
HS3ST3A1	XM_017025480.3 link	c.-791G>T	5_prime_UTR_variant	Exon 1 of 2		XP_016880969.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HS3ST3A1	ENST00000284110.2 link	c.-791G>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 2	1	NM_006042.3	ENSP00000284110.1		Q9Y663
HS3ST3A1	ENST00000284110.2 link	c.-791G>T		5_prime_UTR_variant	Exon 1 of 2	1	NM_006042.3	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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over