19-48598699-C-T

Variant names:

• chr19-48598699-C-T
• rs4149455
• NM_177973.2:c.827-436C>T

Variant summary

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

The NM_177973.2(SULT2B1):​c.827-436C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,792 control chromosomes in the GnomAD database, including 13,721 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 0.41 (13721 hom., cov: 31)
• Consequence: SULT2B1 NM_177973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2	c.827-436C>T		intron_variant	Intron 6 of 6	ENST00000201586.7	NP_814444.1
SULT2B1	NM_004605.2	c.782-436C>T		intron_variant	Intron 5 of 5		NP_004596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT2B1	ENST00000201586.7	c.827-436C>T		intron_variant	Intron 6 of 6	1	NM_177973.2	ENSP00000201586.2
SULT2B1	ENST00000323090.4	c.782-436C>T		intron_variant	Intron 5 of 5	1		ENSP00000312880.3
SULT2B1	ENST00000594274.1	n.577-436C>T		intron_variant	Intron 4 of 4	3
SULT2B1	ENST00000597923.1	n.1135-436C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62728 AN: 151674 Hom.: 13688 Cov.: 31

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.414 AC: 62841 AN: 151792 Hom.: 13721 Cov.: 31 AF XY: 0.418 AC XY: 31010 AN XY: 74158

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.373

Alfa AF: 0.345 Hom.: 12398

Bravo AF: 0.418

Asia WGS AF: 0.414 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.73

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: rs4149455; hg19: chr19-49101956;