19-48589173-A-G

Position:

• chr19-48589173-A-G

Variant summary

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

The NM_177973.2(SULT2B1):​c.423+1736A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,124 control chromosomes in the GnomAD database, including 47,121 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 0.77 (47121 hom., cov: 31)
• Consequence: SULT2B1 NM_177973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT2B1	NM_177973.2	c.423+1736A>G		intron_variant		ENST00000201586.7	NP_814444.1
SULT2B1	NM_004605.2	c.378+1736A>G		intron_variant			NP_004596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT2B1	ENST00000201586.7	c.423+1736A>G		intron_variant		1	NM_177973.2	ENSP00000201586	P2
SULT2B1	ENST00000323090.4	c.378+1736A>G		intron_variant		1		ENSP00000312880	A2
	ENST00000666424.1	n.493+7573T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117699 AN: 152006 Hom.: 47067 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.774 AC: 117810 AN: 152124 Hom.: 47121 Cov.: 31 AF XY: 0.760 AC XY: 56560 AN XY: 74374

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.777

Alfa AF: 0.762 Hom.: 62841

Bravo AF: 0.780

Asia WGS AF: 0.591 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.5
DANN	Benign	0.51

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: rs10426628; hg19: chr19-49092430;