Variant 19-48599256-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

SULT2B1 (HGNC:):

SULT2B1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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/exons	MANE	Protein	UniProt
SULT2B1	NM_177973.2 linkuse as main transcript	c.948C>T	p.Asp316Asp	synonymous_variant	7/7	ENST00000201586.7	NP_814444.1	O00204-1
SULT2B1	NM_004605.2 linkuse as main transcript	c.903C>T	p.Asp301Asp	synonymous_variant	6/6		NP_004596.2	O00204-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SULT2B1	ENST00000201586.7 linkuse as main transcript	c.948C>T	p.Asp316Asp	synonymous_variant	7/7	1	NM_177973.2	ENSP00000201586.2	O00204-1
SULT2B1	ENST00000323090.4 linkuse as main transcript	c.903C>T	p.Asp301Asp	synonymous_variant	6/6	1		ENSP00000312880.3	O00204-2
SULT2B1	ENST00000594274.1 linkuse as main transcript	n.698C>T		non_coding_transcript_exon_variant	5/5	3
SULT2B1	ENST00000597923.1 linkuse as main transcript	n.1256C>T		non_coding_transcript_exon_variant	2/2	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

GnomAD3 exomes

AF:

0.159

AC:

38085

AN:

239312

Hom.:

3870

AF XY:

0.151

AC XY:

19636

AN XY:

130242

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 SAS exome

AF:

0.102

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

Gnomad4 AFR exome

AF:

0.0808

Gnomad4 AMR exome

AF:

0.324

Gnomad4 ASJ exome

AF:

0.0715

Gnomad4 EAS exome

AF:

0.186

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.196

Gnomad4 NFE exome

AF:

0.136

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.132

AC:

20077

AN:

151784

Hom.:

1534

Cov.:

AF XY:

0.136

AC XY:

10093

AN XY:

74144

show subpopulations

Gnomad4 AFR

AF:

0.0825

Gnomad4 AMR

AF:

0.217

Gnomad4 ASJ

AF:

0.0770

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.106

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.124

Hom.:

2038

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

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

SULT2B1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

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

DANN

Benign

0.81

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over