rs3786749

Variant names:

• chr19-48592021-T-C
• rs3786749
• NM_177973.2:c.550+286T>C

Your query was ambiguous. Multiple possible variants found:

• chr19-48592021-T-C
• chr19-48592021-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_177973.2(SULT2B1):​c.550+286T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,122 control chromosomes in the GnomAD database, including 64,024 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 0.91 (64024 hom., cov: 31)
• Consequence: SULT2B1 NM_177973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 9 publications found

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 Gene-Disease associations (from GenCC):

• ichthyosis, congenital, autosomal recessive 14

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: PanelApp Australia, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• lamellar ichthyosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000287603 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2	c.550+286T>C		intron_variant	Intron 4 of 6	ENST00000201586.7	NP_814444.1
SULT2B1	NM_004605.2	c.505+286T>C		intron_variant	Intron 3 of 5		NP_004596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT2B1	ENST00000201586.7	c.550+286T>C		intron_variant	Intron 4 of 6	1	NM_177973.2	ENSP00000201586.2
SULT2B1	ENST00000323090.4	c.505+286T>C		intron_variant	Intron 3 of 5	1		ENSP00000312880.3
SULT2B1	ENST00000594274.1	n.300+286T>C		intron_variant	Intron 2 of 4	3
ENSG00000287603	ENST00000666424.1	n.493+4725A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139069 AN: 152004 Hom.: 63983 Cov.: 31

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.961

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.915 AC: 139166 AN: 152122 Hom.: 64024 Cov.: 31 AF XY: 0.914 AC XY: 67976 AN XY: 74370

African (AFR) AF: 0.829 AC: 34402 AN: 41498

American (AMR) AF: 0.966 AC: 14750 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3403 AN: 3472

East Asian (EAS) AF: 0.776 AC: 3995 AN: 5146

South Asian (SAS) AF: 0.899 AC: 4328 AN: 4814

European-Finnish (FIN) AF: 0.927 AC: 9818 AN: 10594

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.961 AC: 65338 AN: 68010

Other (OTH) AF: 0.935 AC: 1976 AN: 2114

Alfa AF: 0.947 Hom.: 34097

Bravo AF: 0.914

Asia WGS AF: 0.823 AC: 2866 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	0.56
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3786749; hg19: chr19-49095278;