Variant chr19-47879223-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT2A1	NM_003167.4 link	c.473-93C>G		intron_variant		ENST00000222002.4	NP_003158.2	Q06520A8K015

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT2A1	ENST00000222002.4 link	c.473-93C>G		intron_variant		1	NM_003167.4	ENSP00000222002.2		Q06520

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

Gnomad4 AFR exome

AF:

0.0716

Gnomad4 AMR exome

AF:

0.402

Gnomad4 ASJ exome

AF:

0.235

Gnomad4 EAS exome

AF:

0.465

Gnomad4 SAS exome

AF:

0.325

Gnomad4 FIN exome

AF:

0.305

Gnomad4 NFE exome

AF:

0.278

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.241

AC:

36623

AN:

152082

Hom.:

5474

Cov.:

AF XY:

0.251

AC XY:

18630

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.0713

Gnomad4 AMR

AF:

0.354

Gnomad4 ASJ

AF:

0.226

Gnomad4 EAS

AF:

0.486

Gnomad4 SAS

AF:

0.340

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.281

Gnomad4 OTH

AF:

0.265

Alfa

AF:

0.149

Hom.:

314

Bravo

AF:

0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.56

DANN

Benign

0.40

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over