dbSNP rs3760091: SULT1A1:c.-5+452G>C (chr16-28609479-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001055.4(SULT1A1):c.-5+452G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 1,141,004 control chromosomes in the GnomAD database, including 80,245 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 0.38 ( 9428 hom., cov: 37)

Exomes 𝑓: 0.40 ( 70817 hom. )

Consequence

SULT1A1
NM_001055.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

29 publications found

Variant links:

Genes affected

SULT1A1 (HGNC:11453): (sulfotransferase family 1A 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 encodes one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SULT1A1 links:

ENSG00000289755 (HGNC:):

ENSG00000289755 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=-1.09).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1A1	NM_001055.4 link	c.-5+452G>C		intron_variant	Intron 1 of 7	ENST00000314752.12	NP_001046.2	P50225-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1A1	ENST00000314752.12 link	c.-5+452G>C		intron_variant	Intron 1 of 7	1	NM_001055.4	ENSP00000321988.7		P50225-1

Frequencies

GnomAD3 genomes

AF:

0.380

AC:

57251

AN:

150576

Hom.:

9420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.510

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.396

Gnomad OTH

AF:

0.404

GnomAD2 exomes

AF:

0.378

AC:

48484

AN:

128248

AF XY:

0.376

show subpopulations

Gnomad AFR exome

AF:

0.342

Gnomad AMR exome

AF:

0.380

Gnomad ASJ exome

AF:

0.399

Gnomad EAS exome

AF:

0.341

Gnomad FIN exome

AF:

0.434

Gnomad NFE exome

AF:

0.400

Gnomad OTH exome

AF:

0.412

GnomAD4 exome

AF:

0.397

AC:

393604

AN:

990310

Hom.:

70817

Cov.:

AF XY:

0.394

AC XY:

193413

AN XY:

490840

show subpopulations

African (AFR)

AF:

0.358

AC:

8051

AN:

22458

American (AMR)

AF:

0.375

AC:

10159

AN:

27080

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

5931

AN:

14636

East Asian (EAS)

AF:

0.349

AC:

4187

AN:

11986

South Asian (SAS)

AF:

0.326

AC:

23593

AN:

72412

European-Finnish (FIN)

AF:

0.439

AC:

5618

AN:

12790

Middle Eastern (MID)

AF:

0.466

AC:

1916

AN:

4108

European-Non Finnish (NFE)

AF:

0.405

AC:

319489

AN:

788178

Other (OTH)

AF:

0.400

AC:

14660

AN:

36662

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

8555

17111

25666

34222

42777

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11534

23068

34602

46136

57670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.380

AC:

57290

AN:

150694

Hom.:

9428

Cov.:

AF XY:

0.380

AC XY:

28000

AN XY:

73588

show subpopulations

African (AFR)

AF:

0.347

AC:

14229

AN:

40948

American (AMR)

AF:

0.374

AC:

5664

AN:

15152

Ashkenazi Jewish (ASJ)

AF:

0.400

AC:

1385

AN:

3460

East Asian (EAS)

AF:

0.362

AC:

1809

AN:

4998

South Asian (SAS)

AF:

0.314

AC:

1500

AN:

4772

European-Finnish (FIN)

AF:

0.431

AC:

4530

AN:

10500

Middle Eastern (MID)

AF:

0.466

AC:

136

AN:

292

European-Non Finnish (NFE)

AF:

0.396

AC:

26739

AN:

67600

Other (OTH)

AF:

0.405

AC:

840

AN:

2074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1216

2432

3648

4864

6080

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

568

1136

1704

2272

2840

<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:

0.385

Hom.:

1709

Asia WGS

AF:

0.350

AC:

1216

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.054

(source)

DANN

Benign

0.28

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over