rs4788068

chr16-28605402-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.*419G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 284,640 control chromosomes in the GnomAD database, including 15,804 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 (8979 hom., cov: 35)
  • Exomes 𝑓: 0.33 (6825 hom.)
• Consequence: SULT1A1 NM_001055.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.45

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT1A1	NM_001055.4	c.*419G>A		3_prime_UTR_variant	8/8	ENST00000314752.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT1A1	ENST00000314752.12	c.*419G>A		3_prime_UTR_variant	8/8	1	NM_001055.4	P1
SULT1A1	ENST00000569554.5	c.*419G>A		3_prime_UTR_variant	7/7	1		P1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51083 AN: 149974 Hom.: 8970 Cov.: 35

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.329 AC: 44208 AN: 134556 Hom.: 6825 Cov.: 0 AF XY: 0.315 AC XY: 23187 AN XY: 73572

Gnomad4 AFR exome AF: 0.191

Gnomad4 AMR exome AF: 0.409

Gnomad4 ASJ exome AF: 0.281

Gnomad4 EAS exome AF: 0.233

Gnomad4 SAS exome AF: 0.224

Gnomad4 FIN exome AF: 0.428

Gnomad4 NFE exome AF: 0.365

Gnomad4 OTH exome AF: 0.343

GnomAD4 genome AF: 0.341 AC: 51132 AN: 150084 Hom.: 8979 Cov.: 35 AF XY: 0.342 AC XY: 25047 AN XY: 73254

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.317

Alfa AF: 0.381 Hom.: 1242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.42
Dann	Benign	0.46

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: rs4788068; hg19: chr16-28616723;