19-48594630-A-T

Position:

• chr19-48594630-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.645+1814A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,208 control chromosomes in the GnomAD database, including 60,247 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 0.89 (60247 hom., cov: 32)
• Consequence: SULT2B1 NM_177973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935

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 (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 (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT2B1	NM_177973.2	c.645+1814A>T		intron_variant		ENST00000201586.7	NP_814444.1
SULT2B1	NM_004605.2	c.600+1814A>T		intron_variant			NP_004596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT2B1	ENST00000201586.7	c.645+1814A>T		intron_variant		1	NM_177973.2	ENSP00000201586.2
SULT2B1	ENST00000323090.4	c.600+1814A>T		intron_variant		1		ENSP00000312880.3
SULT2B1	ENST00000594274.1	n.395+1814A>T		intron_variant		3
ENSG00000287603	ENST00000666424.1	n.493+2116T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135216 AN: 152090 Hom.: 60194 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.889 AC: 135323 AN: 152208 Hom.: 60247 Cov.: 32 AF XY: 0.891 AC XY: 66265 AN XY: 74392

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.889

Alfa AF: 0.878 Hom.: 32471

Bravo AF: 0.893

Asia WGS AF: 0.953 AC: 3314 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	0.90
DANN	Benign	0.85

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: rs10417472; hg19: chr19-49097887;