19-47883100-A-G

Variant names:

• chr19-47883100-A-G
• rs4149448
• NM_003167.4:c.345+477T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003167.4(SULT2A1):​c.345+477T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,840 control chromosomes in the GnomAD database, including 1,439 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 0.13 (1439 hom., cov: 30)
• Consequence: SULT2A1 NM_003167.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT2A1	NM_003167.4	c.345+477T>C		intron_variant	Intron 2 of 5	ENST00000222002.4	NP_003158.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT2A1	ENST00000222002.4	c.345+477T>C		intron_variant	Intron 2 of 5	1	NM_003167.4	ENSP00000222002.2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19989 AN: 151722 Hom.: 1436 Cov.: 30

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.132 AC: 20022 AN: 151840 Hom.: 1439 Cov.: 30 AF XY: 0.131 AC XY: 9696 AN XY: 74204

African (AFR) AF: 0.185 AC: 7636 AN: 41368

American (AMR) AF: 0.102 AC: 1554 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3468

East Asian (EAS) AF: 0.181 AC: 935 AN: 5154

South Asian (SAS) AF: 0.113 AC: 541 AN: 4802

European-Finnish (FIN) AF: 0.101 AC: 1070 AN: 10564

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7585 AN: 67956

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.118 Hom.: 1759

Bravo AF: 0.135

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.63
DANN	Benign	0.42
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4149448; hg19: chr19-48386357;