rs750155

chr16-28609251-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.-4-392G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,242,994 control chromosomes in the GnomAD database, including 134,960 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 0.45 (14814 hom., cov: 38)
  • Exomes 𝑓: 0.47 (120146 hom.)
• Consequence: SULT1A1 NM_001055.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT1A1	NM_001055.4	c.-4-392G>A		intron_variant		ENST00000314752.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT1A1	ENST00000314752.12	c.-4-392G>A		intron_variant		1	NM_001055.4	P1
SULT1A1	ENST00000566189.5	c.-35-361G>A		intron_variant		5
SULT1A1	ENST00000567512.1	c.-4-392G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.449 AC: 67576 AN: 150432 Hom.: 14796 Cov.: 38

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.421

GnomAD4 exome AF: 0.473 AC: 517035 AN: 1092444 Hom.: 120146 Cov.: 38 AF XY: 0.469 AC XY: 247950 AN XY: 528860

Gnomad4 AFR exome AF: 0.341

Gnomad4 AMR exome AF: 0.534

Gnomad4 ASJ exome AF: 0.407

Gnomad4 EAS exome AF: 0.462

Gnomad4 SAS exome AF: 0.316

Gnomad4 FIN exome AF: 0.558

Gnomad4 NFE exome AF: 0.488

Gnomad4 OTH exome AF: 0.457

GnomAD4 genome AF: 0.449 AC: 67648 AN: 150550 Hom.: 14814 Cov.: 38 AF XY: 0.451 AC XY: 33161 AN XY: 73544

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.423

Alfa AF: 0.315 Hom.: 685

Asia WGS AF: 0.396 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.2
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750155; hg19: chr16-28620572; COSMIC: COSV59088117; COSMIC: COSV59088117;