rs3760802

chr19-48573430-G-Achr19-48573430-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_177973.2(SULT2B1):c.72-2511G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,858 control chromosomes in the GnomAD database, including 15,140 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (15140 hom., cov: 31)
• Consequence: SULT2B1 NM_177973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT2B1	NM_177973.2	c.72-2511G>A		intron_variant		ENST00000201586.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT2B1	ENST00000201586.7	c.72-2511G>A		intron_variant		1	NM_177973.2	P2
	ENST00000666424.1	n.494-22897C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66427 AN: 151738 Hom.: 15147 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.442

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.437 AC: 66433 AN: 151858 Hom.: 15140 Cov.: 31 AF XY: 0.441 AC XY: 32694 AN XY: 74186

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.442

Alfa AF: 0.487 Hom.: 23454

Bravo AF: 0.422

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.5
Dann	Benign	0.61

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: rs3760802; hg19: chr19-49076687;