Genetic Variant NM_003167.4:c.473-93C>G (chr19-47879223-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_003167.4(SULT2A1):c.473-93C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 761,944 control chromosomes in the GnomAD database, including 33,789 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.24 ( 5474 hom., cov: 31)

Exomes 𝑓: 0.30 ( 28315 hom. )

Consequence

SULT2A1
NM_003167.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.572

Publications

10 publications found

Variant links:

Genes affected

SULT2A1 (HGNC:11458): (sulfotransferase family 2A member 1) This gene encodes a member of the sulfotransferase family. Sulfotransferases aid in the metabolism of drugs and endogenous compounds by converting these substances into more hydrophilic water-soluble sulfate conjugates that can be easily excreted. This protein catalyzes the sulfation of steroids and bile acids in the liver and adrenal glands, and may have a role in the inherited adrenal androgen excess in women with polycystic ovary syndrome. [provided by RefSeq, Mar 2010]

SULT2A1 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003167.4. 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
	SULT2A1	NM_003167.4	MANE Select	c.473-93C>G		intron	N/A	NP_003158.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SULT2A1	ENST00000222002.4	TSL:1 MANE Select	c.473-93C>G	intron	N/A	ENSP00000222002.2	Q06520
SULT2A1	ENST00000903238.1		c.473-93C>G	intron	N/A	ENSP00000573297.1
SULT2A1	ENST00000903236.1		c.472+2861C>G	intron	N/A	ENSP00000573295.1

Frequencies

GnomAD3 genomes

AF:

0.241

AC:

36644

AN:

151964

Hom.:

5484

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0714

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.486

Gnomad SAS

AF:

0.340

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.268

GnomAD4 exome

AF:

0.296

AC:

180385

AN:

609862

Hom.:

28315

AF XY:

0.297

AC XY:

97167

AN XY:

327088

show subpopulations

African (AFR)

AF:

0.0716

AC:

1178

AN:

16442

American (AMR)

AF:

0.402

AC:

13671

AN:

34028

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

4272

AN:

18142

East Asian (EAS)

AF:

0.465

AC:

16355

AN:

35192

South Asian (SAS)

AF:

0.325

AC:

20255

AN:

62378

European-Finnish (FIN)

AF:

0.305

AC:

14229

AN:

46640

Middle Eastern (MID)

AF:

0.273

AC:

1077

AN:

3946

European-Non Finnish (NFE)

AF:

0.278

AC:

100349

AN:

361502

Other (OTH)

AF:

0.285

AC:

8999

AN:

31592

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

5926

11852

17778

23704

29630

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1226

2452

3678

4904

6130

<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:

0.241

AC:

36623

AN:

152082

Hom.:

5474

Cov.:

AF XY:

0.251

AC XY:

18630

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.0713

AC:

2959

AN:

41528

American (AMR)

AF:

0.354

AC:

5402

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

783

AN:

3472

East Asian (EAS)

AF:

0.486

AC:

2508

AN:

5162

South Asian (SAS)

AF:

0.340

AC:

1636

AN:

4814

European-Finnish (FIN)

AF:

0.318

AC:

3351

AN:

10546

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.281

AC:

19081

AN:

67978

Other (OTH)

AF:

0.265

AC:

559

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1352

2704

4055

5407

6759

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<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:

0.149

Hom.:

314

Bravo

AF:

0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.56

(source)

DANN

Benign

0.40

PhyloP100

-0.57

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over