Genetic Variant SULT2B1:c.214+2144G>C (chr19-48578227-G-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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.229

Publications

3 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=-0.81).

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 rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2 link	c.214+2144G>C		intron_variant	Intron 2 of 6	ENST00000201586.7	NP_814444.1	O00204-1
SULT2B1	NM_004605.2 link	c.169+2144G>C		intron_variant	Intron 1 of 5		NP_004596.2	O00204-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SULT2B1	ENST00000201586.7 link	c.214+2144G>C	intron_variant	Intron 2 of 6	1	NM_177973.2	ENSP00000201586.2	O00204-1
SULT2B1	ENST00000323090.4 link	c.169+2144G>C	intron_variant	Intron 1 of 5	1		ENSP00000312880.3	O00204-2
ENSG00000287603	ENST00000666424.1 link	n.493+18519C>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.461

AC:

69859

AN:

151610

Hom.:

16532

Cov.:

show subpopulations

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.:

AF XY:

0.463

AC XY:

34332

AN XY:

74098

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1883

3766

5650

7533

9416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

662

1324

1986

2648

3310

<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:

0.369

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

(source)

DANN

Benign

0.78

PhyloP100

0.23

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