rs3760091

Positions:

• chr16-28609479-C-G
• chr16-28609479-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SULT1A1	NM_001055.4	c.-5+452G>C		intron_variant		ENST00000314752.12	NP_001046.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1A1	ENST00000314752.12	c.-5+452G>C		intron_variant		1	NM_001055.4	ENSP00000321988	P1
SULT1A1	ENST00000566189.5	c.-36+452G>C		intron_variant		5		ENSP00000456459
SULT1A1	ENST00000567512.1	c.-5+452G>C		intron_variant		3		ENSP00000455979

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57251 AN: 150576 Hom.: 9420 Cov.: 37

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

GnomAD3 exomes AF: 0.378 AC: 48484 AN: 128248 Hom.: 8168 AF XY: 0.376 AC XY: 26261 AN XY: 69790

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 SAS exome AF: 0.325

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.: 15 AF XY: 0.394 AC XY: 193413 AN XY: 490840

Gnomad4 AFR exome AF: 0.358

Gnomad4 AMR exome AF: 0.375

Gnomad4 ASJ exome AF: 0.405

Gnomad4 EAS exome AF: 0.349

Gnomad4 SAS exome AF: 0.326

Gnomad4 FIN exome AF: 0.439

Gnomad4 NFE exome AF: 0.405

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.380 AC: 57290 AN: 150694 Hom.: 9428 Cov.: 37 AF XY: 0.380 AC XY: 28000 AN XY: 73588

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.405

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
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760091; hg19: chr16-28620800; COSMIC: COSV59086574; COSMIC: COSV59086574;