Genetic Variant SULT2B1:c.827-436C>T (chr19-48598699-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.578

Publications

14 publications found

Variant links:

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: G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics
lamellar ichthyosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

SULT2B1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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.827-436C>T		intron	N/A	NP_814444.1	O00204-1
	SULT2B1	NM_004605.2		c.782-436C>T		intron	N/A	NP_004596.2	O00204-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SULT2B1	ENST00000201586.7	TSL:1 MANE Select	c.827-436C>T	intron	N/A	ENSP00000201586.2	O00204-1
SULT2B1	ENST00000323090.4	TSL:1	c.782-436C>T	intron	N/A	ENSP00000312880.3	O00204-2
SULT2B1	ENST00000594274.1	TSL:3	n.577-436C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62728

AN:

151674

Hom.:

13688

Cov.:

show subpopulations

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.:

AF XY:

0.418

AC XY:

31010

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.542

AC:

22417

AN:

41346

American (AMR)

AF:

0.402

AC:

6134

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

1073

AN:

3470

East Asian (EAS)

AF:

0.482

AC:

2478

AN:

5142

South Asian (SAS)

AF:

0.338

AC:

1627

AN:

4820

European-Finnish (FIN)

AF:

0.464

AC:

4877

AN:

10516

Middle Eastern (MID)

AF:

0.205

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.339

AC:

23015

AN:

67946

Other (OTH)

AF:

0.373

AC:

786

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1780

3560

5341

7121

8901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

586

1172

1758

2344

2930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.354

Hom.:

16662

Bravo

AF:

0.418

Asia WGS

AF:

0.414

AC:

1440

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.9

(source)

DANN

Benign

0.73

PhyloP100

-0.58

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over