Variant chr19-48575989-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.120C>T(p.Pro40=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,613,536 control chromosomes in the GnomAD database, including 20,560 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2214 hom., cov: 30)

Exomes 𝑓: 0.15 ( 18346 hom. )

Consequence

SULT2B1
NM_177973.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.55

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 19-48575989-C-T is Benign according to our data. Variant chr19-48575989-C-T is described in ClinVar as [Benign]. Clinvar id is 1613054.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.55 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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.120C>T	p.Pro40=	synonymous_variant	2/7	ENST00000201586.7	NP_814444.1
SULT2B1	NM_004605.2 linkuse as main transcript	c.75C>T	p.Pro25=	synonymous_variant	1/6		NP_004596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT2B1	ENST00000201586.7 linkuse as main transcript	c.120C>T	p.Pro40=	synonymous_variant	2/7	1	NM_177973.2	ENSP00000201586	P2	O00204-1
SULT2B1	ENST00000323090.4 linkuse as main transcript	c.75C>T	p.Pro25=	synonymous_variant	1/6	1		ENSP00000312880	A2	O00204-2
	ENST00000666424.1 linkuse as main transcript	n.493+20757G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.160

AC:

24232

AN:

151884

Hom.:

2214

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.155

GnomAD3 exomes

AF:

0.130

AC:

32296

AN:

248900

Hom.:

2453

AF XY:

0.132

AC XY:

17769

AN XY:

134738

show subpopulations

Gnomad AFR exome

AF:

0.224

Gnomad AMR exome

AF:

0.0720

Gnomad ASJ exome

AF:

0.177

Gnomad EAS exome

AF:

0.00256

Gnomad SAS exome

AF:

0.127

Gnomad FIN exome

AF:

0.112

Gnomad NFE exome

AF:

0.155

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.154

AC:

225448

AN:

1461536

Hom.:

18346

Cov.:

AF XY:

0.153

AC XY:

111531

AN XY:

727074

show subpopulations

Gnomad4 AFR exome

AF:

0.223

Gnomad4 AMR exome

AF:

0.0770

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.000907

Gnomad4 SAS exome

AF:

0.129

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.164

Gnomad4 OTH exome

AF:

0.155

GnomAD4 genome

AF:

0.160

AC:

24256

AN:

152000

Hom.:

2214

Cov.:

AF XY:

0.156

AC XY:

11608

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.222

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.00213

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.106

Gnomad4 NFE

AF:

0.158

Gnomad4 OTH

AF:

0.153

Alfa

AF:

0.159

Hom.:

4061

Bravo

AF:

0.161

Asia WGS

AF:

0.0630

AC:

219

AN:

3478

EpiCase

AF:

0.157

EpiControl

AF:

0.159

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 22, 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

-0.61

CADD

Benign

2.7

DANN

Benign

0.84

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