Genetic Variant SULT2B1:c.645+1814A>T (chr19-48594630-A-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.645+1814A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,208 control chromosomes in the GnomAD database, including 60,247 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 0.89 ( 60247 hom., cov: 32)

Consequence

SULT2B1
NM_177973.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.935

Publications

5 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:

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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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) 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.645+1814A>T		intron_variant	Intron 5 of 6	ENST00000201586.7	NP_814444.1	O00204-1
SULT2B1	NM_004605.2 link	c.600+1814A>T		intron_variant	Intron 4 of 5		NP_004596.2	O00204-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SULT2B1	ENST00000201586.7 link	c.645+1814A>T	intron_variant	Intron 5 of 6	1	NM_177973.2	ENSP00000201586.2	O00204-1
SULT2B1	ENST00000323090.4 link	c.600+1814A>T	intron_variant	Intron 4 of 5	1		ENSP00000312880.3	O00204-2
SULT2B1	ENST00000594274.1 link	n.395+1814A>T	intron_variant	Intron 3 of 4	3
ENSG00000287603	ENST00000666424.1 link	n.493+2116T>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.889

AC:

135216

AN:

152090

Hom.:

60194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.906

Gnomad AMI

AF:

0.928

Gnomad AMR

AF:

0.912

Gnomad ASJ

AF:

0.836

Gnomad EAS

AF:

0.991

Gnomad SAS

AF:

0.926

Gnomad FIN

AF:

0.864

Gnomad MID

AF:

0.883

Gnomad NFE

AF:

0.869

Gnomad OTH

AF:

0.893

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

GnomAD4 genome

AF:

0.889

AC:

135323

AN:

152208

Hom.:

60247

Cov.:

AF XY:

0.891

AC XY:

66265

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.906

AC:

37651

AN:

41540

American (AMR)

AF:

0.912

AC:

13927

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.836

AC:

2902

AN:

3472

East Asian (EAS)

AF:

0.991

AC:

5129

AN:

5178

South Asian (SAS)

AF:

0.926

AC:

4467

AN:

4822

European-Finnish (FIN)

AF:

0.864

AC:

9146

AN:

10588

Middle Eastern (MID)

AF:

0.881

AC:

259

AN:

294

European-Non Finnish (NFE)

AF:

0.869

AC:

59119

AN:

68022

Other (OTH)

AF:

0.889

AC:

1877

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

772

1544

2316

3088

3860

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

902

1804

2706

3608

4510

<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:

0.878

Hom.:

32471

Bravo

AF:

0.893

Asia WGS

AF:

0.953

AC:

3314

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.90

(source)

DANN

Benign

0.85

PhyloP100

-0.94

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