19-48599256-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_177973.2(SULT2B1):c.948C>T(p.Asp316Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,609,242 control chromosomes in the GnomAD database, including 17,103 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1534 hom., cov: 31)

Exomes 𝑓: 0.14 ( 15569 hom. )

Consequence

SULT2B1
NM_177973.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.343

Publications

23 publications found

Variant links:

Genes affected

SULT2B1 (HGNC:11459): (sulfotransferase family 2B member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene sulfates dehydroepiandrosterone but not 4-nitrophenol, a typical substrate for the phenol and estrogen sulfotransferase subfamilies. Two alternatively spliced variants that encode different isoforms have been described. [provided by RefSeq, Jul 2008]

SULT2B1 Gene-Disease associations (from GenCC):

ichthyosis, congenital, autosomal recessive 14
Inheritance: AR Classification: STRONG, LIMITED Submitted by: PanelApp Australia, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
lamellar ichthyosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

SULT2B1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 19-48599256-C-T is Benign according to our data. Variant chr19-48599256-C-T is described in ClinVar as Benign. ClinVar VariationId is 1601174.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.343 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2 link	c.948C>T	p.Asp316Asp	synonymous_variant	Exon 7 of 7	ENST00000201586.7	NP_814444.1	O00204-1
SULT2B1	NM_004605.2 link	c.903C>T	p.Asp301Asp	synonymous_variant	Exon 6 of 6		NP_004596.2	O00204-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SULT2B1	ENST00000201586.7 link	c.948C>T	p.Asp316Asp	synonymous_variant	Exon 7 of 7	1	NM_177973.2	ENSP00000201586.2	O00204-1
SULT2B1	ENST00000323090.4 link	c.903C>T	p.Asp301Asp	synonymous_variant	Exon 6 of 6	1		ENSP00000312880.3	O00204-2
SULT2B1	ENST00000594274.1 link	n.698C>T		non_coding_transcript_exon_variant	Exon 5 of 5	3
SULT2B1	ENST00000597923.1 link	n.1256C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

20038

AN:

151668

Hom.:

1526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0824

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.216

Gnomad ASJ

AF:

0.0770

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.135

GnomAD2 exomes

AF:

0.159

AC:

38085

AN:

239312

AF XY:

0.151

show subpopulations

Gnomad AFR exome

AF:

0.0828

Gnomad AMR exome

AF:

0.337

Gnomad ASJ exome

AF:

0.0746

Gnomad EAS exome

AF:

0.151

Gnomad FIN exome

AF:

0.192

Gnomad NFE exome

AF:

0.134

Gnomad OTH exome

AF:

0.145

GnomAD4 exome

AF:

0.140

AC:

203501

AN:

1457458

Hom.:

15569

Cov.:

AF XY:

0.138

AC XY:

99831

AN XY:

724738

show subpopulations

African (AFR)

AF:

0.0808

AC:

2700

AN:

33418

American (AMR)

AF:

0.324

AC:

14265

AN:

44022

Ashkenazi Jewish (ASJ)

AF:

0.0715

AC:

1857

AN:

25960

East Asian (EAS)

AF:

0.186

AC:

7382

AN:

39582

South Asian (SAS)

AF:

0.101

AC:

8615

AN:

85624

European-Finnish (FIN)

AF:

0.196

AC:

10255

AN:

52446

Middle Eastern (MID)

AF:

0.0732

AC:

421

AN:

5754

European-Non Finnish (NFE)

AF:

0.136

AC:

150562

AN:

1110460

Other (OTH)

AF:

0.124

AC:

7444

AN:

60192

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

10009

20018

30026

40035

50044

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5566

11132

16698

22264

27830

<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:

0.132

AC:

20077

AN:

151784

Hom.:

1534

Cov.:

AF XY:

0.136

AC XY:

10093

AN XY:

74144

show subpopulations

African (AFR)

AF:

0.0825

AC:

3418

AN:

41420

American (AMR)

AF:

0.217

AC:

3295

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.0770

AC:

267

AN:

3468

East Asian (EAS)

AF:

0.160

AC:

819

AN:

5126

South Asian (SAS)

AF:

0.106

AC:

511

AN:

4802

European-Finnish (FIN)

AF:

0.200

AC:

2103

AN:

10538

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.135

AC:

9186

AN:

67920

Other (OTH)

AF:

0.135

AC:

285

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

858

1716

2573

3431

4289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

218

436

654

872

1090

<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:

0.127

Hom.:

2801

Bravo

AF:

0.138

Asia WGS

AF:

0.136

AC:

474

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

SULT2B1-related disorder

Benign:1

Oct 21, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

1.1

(source)

DANN

Benign

0.81

PhyloP100

-0.34

Mutation Taster

=100/0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over