rs1042157

Positions:

• chr16-28605736-G-A
• chr16-28605736-G-C

Variant summary

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

The ENST00000314752.12(SULT1A1):​c.*85C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,576,354 control chromosomes in the GnomAD database, including 108,856 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 0.34 (9039 hom., cov: 36)
  • Exomes 𝑓: 0.38 (99817 hom.)
• Consequence: SULT1A1 ENST00000314752.12 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1A1	NM_001055.4	c.*85C>T		3_prime_UTR_variant	8/8	ENST00000314752.12	NP_001046.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1A1	ENST00000314752.12	c.*85C>T		3_prime_UTR_variant	8/8	1	NM_001055.4	ENSP00000321988	P1
SULT1A1	ENST00000569554.5	c.*85C>T		3_prime_UTR_variant	7/7	1		ENSP00000457912	P1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51215 AN: 150042 Hom.: 9030 Cov.: 36

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.314

GnomAD4 exome AF: 0.375 AC: 535444 AN: 1426204 Hom.: 99817 Cov.: 33 AF XY: 0.372 AC XY: 263556 AN XY: 708640

Gnomad4 AFR exome AF: 0.230

Gnomad4 AMR exome AF: 0.479

Gnomad4 ASJ exome AF: 0.298

Gnomad4 EAS exome AF: 0.215

Gnomad4 SAS exome AF: 0.241

Gnomad4 FIN exome AF: 0.462

Gnomad4 NFE exome AF: 0.391

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.341 AC: 51263 AN: 150150 Hom.: 9039 Cov.: 36 AF XY: 0.343 AC XY: 25147 AN XY: 73340

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.314

Alfa AF: 0.330 Hom.: 1775

Asia WGS AF: 0.284 AC: 985 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	2.1
DANN	Benign	0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1042157; hg19: chr16-28617057; COSMIC: COSV59087578; COSMIC: COSV59087578;