19-48578227-G-C

Variant names:

• chr19-48578227-G-C
• rs10424237
• NM_177973.2:c.214+2144G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_177973.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT2B1	NM_177973.2	MANE Select	c.214+2144G>C		intron	N/A	NP_814444.1	O00204-1
	SULT2B1	NM_004605.2		c.169+2144G>C		intron	N/A	NP_004596.2	O00204-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT2B1	ENST00000201586.7	TSL:1 MANE Select	c.214+2144G>C		intron	N/A	ENSP00000201586.2	O00204-1
	SULT2B1	ENST00000323090.4	TSL:1	c.169+2144G>C		intron	N/A	ENSP00000312880.3	O00204-2
	ENSG00000287603	ENST00000666424.1		n.493+18519C>G		intron	N/A

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

African (AFR) AF: 0.363 AC: 15038 AN: 41394

American (AMR) AF: 0.430 AC: 6539 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1805 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1835 AN: 5130

South Asian (SAS) AF: 0.587 AC: 2821 AN: 4806

European-Finnish (FIN) AF: 0.495 AC: 5204 AN: 10514

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.517 AC: 35142 AN: 67928

Other (OTH) AF: 0.464 AC: 976 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.23
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: rs10424237; hg19: chr19-49081484;