rs750155

Variant names:

• chr16-28609251-C-T
• rs750155
• NM_001055.4:c.-4-392G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 publications found

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]

ENSG00000289755 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SULT1A1	NM_001055.4	c.-4-392G>A		intron_variant	Intron 1 of 7	ENST00000314752.12	NP_001046.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1A1	ENST00000314752.12	c.-4-392G>A		intron_variant	Intron 1 of 7	1	NM_001055.4	ENSP00000321988.7

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

African (AFR) AF: 0.341 AC: 8246 AN: 24148

American (AMR) AF: 0.534 AC: 8529 AN: 15980

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 5106 AN: 12548

East Asian (EAS) AF: 0.462 AC: 7652 AN: 16558

South Asian (SAS) AF: 0.316 AC: 19973 AN: 63164

European-Finnish (FIN) AF: 0.558 AC: 6846 AN: 12266

Middle Eastern (MID) AF: 0.366 AC: 1100 AN: 3006

European-Non Finnish (NFE) AF: 0.488 AC: 440899 AN: 903900

Other (OTH) AF: 0.457 AC: 18684 AN: 40874

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

African (AFR) AF: 0.356 AC: 14585 AN: 40932

American (AMR) AF: 0.482 AC: 7267 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1419 AN: 3458

East Asian (EAS) AF: 0.441 AC: 2256 AN: 5118

South Asian (SAS) AF: 0.308 AC: 1466 AN: 4764

European-Finnish (FIN) AF: 0.571 AC: 5989 AN: 10496

Middle Eastern (MID) AF: 0.337 AC: 97 AN: 288

European-Non Finnish (NFE) AF: 0.494 AC: 33315 AN: 67432

Other (OTH) AF: 0.423 AC: 876 AN: 2070

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
PhyloP100		-0.34
PromoterAI		-0.10	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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