19-48578227-G-C

Position:

• chr19-48578227-G-C

Variant summary

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

The NM_177973.2(SULT2B1):​c.214+2144G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,728 control chromosomes in the GnomAD database, including 16,529 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 0.46 (16529 hom., cov: 30)
• Consequence: SULT2B1 NM_177973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT2B1	NM_177973.2	c.214+2144G>C		intron_variant		ENST00000201586.7	NP_814444.1
SULT2B1	NM_004605.2	c.169+2144G>C		intron_variant			NP_004596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT2B1	ENST00000201586.7	c.214+2144G>C		intron_variant		1	NM_177973.2	ENSP00000201586	P2
SULT2B1	ENST00000323090.4	c.169+2144G>C		intron_variant		1		ENSP00000312880	A2
	ENST00000666424.1	n.493+18519C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69859 AN: 151610 Hom.: 16532 Cov.: 30

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.461 AC: 69876 AN: 151728 Hom.: 16529 Cov.: 30 AF XY: 0.463 AC XY: 34332 AN XY: 74098

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.464

Alfa AF: 0.369 Hom.: 1071

Bravo AF: 0.446

Asia WGS AF: 0.452 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.78

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: rs10424237; hg19: chr19-49081484;