rs12460535

chr19-48595493-A-Gchr19-48595493-A-T

Variant summary

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

The NM_177973.2(SULT2B1):c.646-1246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,806 control chromosomes in the GnomAD database, including 26,551 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 0.58 (26551 hom., cov: 29)
• Consequence: SULT2B1 NM_177973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.776

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT2B1	NM_177973.2	c.646-1246A>G		intron_variant		ENST00000201586.7
SULT2B1	NM_004605.2	c.601-1246A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT2B1	ENST00000201586.7	c.646-1246A>G		intron_variant		1	NM_177973.2	P2
SULT2B1	ENST00000323090.4	c.601-1246A>G		intron_variant		1		A2
	ENST00000666424.1	n.493+1253T>C		intron_variant, non_coding_transcript_variant
SULT2B1	ENST00000594274.1	n.396-1246A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87714 AN: 151690 Hom.: 26551 Cov.: 29

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.578 AC: 87745 AN: 151806 Hom.: 26551 Cov.: 29 AF XY: 0.577 AC XY: 42794 AN XY: 74134

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.615

Alfa AF: 0.645 Hom.: 65889

Bravo AF: 0.584

Asia WGS AF: 0.463 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.9
Dann	Benign	0.69

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: rs12460535; hg19: chr19-49098750;