NM_177973.2:c.120C>T

Variant names:

• chr19-48575989-C-T
• rs2544794
• NM_177973.2:c.120C>T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_177973.2(SULT2B1):​c.120C>T​(p.Pro40Pro) 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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -2.55

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]

ENSG00000287603 (HGNC:):

ACMG classification

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 rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2	c.120C>T	p.Pro40Pro	synonymous_variant	Exon 2 of 7	ENST00000201586.7	NP_814444.1
SULT2B1	NM_004605.2	c.75C>T	p.Pro25Pro	synonymous_variant	Exon 1 of 6		NP_004596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT2B1	ENST00000201586.7	c.120C>T	p.Pro40Pro	synonymous_variant	Exon 2 of 7	1	NM_177973.2	ENSP00000201586.2
SULT2B1	ENST00000323090.4	c.75C>T	p.Pro25Pro	synonymous_variant	Exon 1 of 6	1		ENSP00000312880.3
ENSG00000287603	ENST00000666424.1	n.493+20757G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24232 AN: 151884 Hom.: 2214 Cov.: 30

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

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.: 32 AF XY: 0.153 AC XY: 111531 AN XY: 727074

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.: 30 AF XY: 0.156 AC XY: 11608 AN XY: 74306

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

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

SULT2B1-related disorder Benign:1

Oct 22, 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	-0.61
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

Other links and lift over

dbSNP: rs2544794; hg19: chr19-49079246;