Genetic Variant SULT2B1:c.215-2819T>C (chr19-48584410-T-C) – 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.215-2819T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,250 control chromosomes in the GnomAD database, including 66,814 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 0.94 ( 66814 hom., cov: 33)

Consequence

SULT2B1
NM_177973.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.05

Publications

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

SULT2B1 links:

ENSG00000287603 (HGNC:):

ENSG00000287603 links:

Genome browser will be placed here

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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2 link	c.215-2819T>C		intron_variant	Intron 2 of 6	ENST00000201586.7	NP_814444.1
SULT2B1	NM_004605.2 link	c.170-2819T>C		intron_variant	Intron 1 of 5		NP_004596.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
SULT2B1	ENST00000201586.7 link	c.215-2819T>C	intron_variant	Intron 2 of 6	1	NM_177973.2	ENSP00000201586.2
SULT2B1	ENST00000323090.4 link	c.170-2819T>C	intron_variant	Intron 1 of 5	1		ENSP00000312880.3
ENSG00000287603	ENST00000666424.1 link	n.493+12336A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.936

AC:

142333

AN:

152132

Hom.:

66762

Cov.:

show subpopulations

Gnomad AFR

AF:

0.976

Gnomad AMI

AF:

0.803

Gnomad AMR

AF:

0.845

Gnomad ASJ

AF:

0.957

Gnomad EAS

AF:

0.833

Gnomad SAS

AF:

0.900

Gnomad FIN

AF:

0.940

Gnomad MID

AF:

0.940

Gnomad NFE

AF:

0.942

Gnomad OTH

AF:

0.924

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

GnomAD4 genome

AF:

0.936

AC:

142442

AN:

152250

Hom.:

66814

Cov.:

AF XY:

0.934

AC XY:

69486

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.976

AC:

40590

AN:

41570

American (AMR)

AF:

0.845

AC:

12884

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.957

AC:

3322

AN:

3472

East Asian (EAS)

AF:

0.833

AC:

4311

AN:

5178

South Asian (SAS)

AF:

0.900

AC:

4344

AN:

4824

European-Finnish (FIN)

AF:

0.940

AC:

9969

AN:

10606

Middle Eastern (MID)

AF:

0.935

AC:

275

AN:

294

European-Non Finnish (NFE)

AF:

0.942

AC:

64068

AN:

68032

Other (OTH)

AF:

0.921

AC:

1948

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

470

940

1411

1881

2351

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

910

1820

2730

3640

4550

<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:

0.933

Hom.:

125230

Bravo

AF:

0.931

Asia WGS

AF:

0.858

AC:

2984

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.1

(source)

DANN

Benign

0.49

PhyloP100

-3.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over