NM_177973.2:c.424-10C>T

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_177973.2(SULT2B1):c.424-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 1,608,084 control chromosomes in the GnomAD database, including 3,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.038 ( 250 hom., cov: 31)

Exomes 𝑓: 0.045 ( 2902 hom. )

Consequence

SULT2B1
NM_177973.2 intron

Scores

Splicing: ADA: 0.0005432

Clinical Significance

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

Conservation

PhyloP100: 0.704

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:

ENSG00000287603 (HGNC:):

ENSG00000287603 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 19-48591599-C-T is Benign according to our data. Variant chr19-48591599-C-T is described in ClinVar as [Benign]. Clinvar id is 1601562.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2 link	c.424-10C>T		intron_variant	Intron 3 of 6	ENST00000201586.7	NP_814444.1	O00204-1
SULT2B1	NM_004605.2 link	c.379-10C>T		intron_variant	Intron 2 of 5		NP_004596.2	O00204-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SULT2B1	ENST00000201586.7 link	c.424-10C>T	intron_variant	Intron 3 of 6	1	NM_177973.2	ENSP00000201586.2	O00204-1
SULT2B1	ENST00000323090.4 link	c.379-10C>T	intron_variant	Intron 2 of 5	1		ENSP00000312880.3	O00204-2
SULT2B1	ENST00000594274.1 link	n.174-10C>T	intron_variant	Intron 1 of 4	3
ENSG00000287603	ENST00000666424.1 link	n.493+5147G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0380

AC:

5781

AN:

152028

Hom.:

249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00787

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0635

Gnomad ASJ

AF:

0.0444

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.0910

Gnomad FIN

AF:

0.0371

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0346

Gnomad OTH

AF:

0.0384

GnomAD3 exomes

AF:

0.0599

AC:

14776

AN:

246792

Hom.:

789

AF XY:

0.0577

AC XY:

7685

AN XY:

133290

show subpopulations

Gnomad AFR exome

AF:

0.00734

Gnomad AMR exome

AF:

0.102

Gnomad ASJ exome

AF:

0.0421

Gnomad EAS exome

AF:

0.191

Gnomad SAS exome

AF:

0.0867

Gnomad FIN exome

AF:

0.0370

Gnomad NFE exome

AF:

0.0324

Gnomad OTH exome

AF:

0.0492

GnomAD4 exome

AF:

0.0452

AC:

65826

AN:

1455938

Hom.:

2902

Cov.:

AF XY:

0.0456

AC XY:

33048

AN XY:

724068

show subpopulations

Gnomad4 AFR exome

AF:

0.00632

Gnomad4 AMR exome

AF:

0.0986

Gnomad4 ASJ exome

AF:

0.0416

Gnomad4 EAS exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.0800

Gnomad4 FIN exome

AF:

0.0369

Gnomad4 NFE exome

AF:

0.0347

Gnomad4 OTH exome

AF:

0.0490

GnomAD4 genome

AF:

0.0380

AC:

5787

AN:

152146

Hom.:

250

Cov.:

AF XY:

0.0397

AC XY:

2949

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.00785

Gnomad4 AMR

AF:

0.0636

Gnomad4 ASJ

AF:

0.0444

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.0911

Gnomad4 FIN

AF:

0.0371

Gnomad4 NFE

AF:

0.0346

Gnomad4 OTH

AF:

0.0413

Alfa

AF:

0.0361

Hom.:

253

Bravo

AF:

0.0392

Asia WGS

AF:

0.192

AC:

668

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jan 20, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

SULT2B1-related disorder

Benign:1

Dec 05, 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

-0.76

CADD

Benign

6.9

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00054

dbscSNV1_RF

Benign

0.016

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