16-28605807-T-C

Position:

• chr16-28605807-T-C

Variant summary

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

The NM_001055.4(SULT1A1):​c.*14A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,596,498 control chromosomes in the GnomAD database, including 99,636 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 0.30 (7958 hom., cov: 35)
  • Exomes 𝑓: 0.34 (91678 hom.)
• Consequence: SULT1A1 NM_001055.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1A1	NM_001055.4	c.*14A>G		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.*14A>G		3_prime_UTR_variant	8/8	1	NM_001055.4	ENSP00000321988	P1
SULT1A1	ENST00000569554.5	c.*14A>G		3_prime_UTR_variant	7/7	1		ENSP00000457912	P1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45359 AN: 150230 Hom.: 7950 Cov.: 35

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0745

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.170

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.266

GnomAD3 exomes AF: 0.311 AC: 77013 AN: 247864 Hom.: 13944 AF XY: 0.305 AC XY: 40857 AN XY: 133960

Gnomad AFR exome AF: 0.229

Gnomad AMR exome AF: 0.381

Gnomad ASJ exome AF: 0.253

Gnomad EAS exome AF: 0.0684

Gnomad SAS exome AF: 0.205

Gnomad FIN exome AF: 0.451

Gnomad NFE exome AF: 0.347

Gnomad OTH exome AF: 0.313

GnomAD4 exome AF: 0.337 AC: 487685 AN: 1446160 Hom.: 91678 Cov.: 39 AF XY: 0.334 AC XY: 240152 AN XY: 719516

Gnomad4 AFR exome AF: 0.221

Gnomad4 AMR exome AF: 0.385

Gnomad4 ASJ exome AF: 0.248

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.206

Gnomad4 FIN exome AF: 0.450

Gnomad4 NFE exome AF: 0.356

Gnomad4 OTH exome AF: 0.307

GnomAD4 genome AF: 0.302 AC: 45409 AN: 150338 Hom.: 7958 Cov.: 35 AF XY: 0.303 AC XY: 22231 AN XY: 73448

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0747

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.265

Alfa AF: 0.336 Hom.: 1990

Bravo AF: 0.292

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.64

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: rs6839; hg19: chr16-28617128; COSMIC: COSV59086309; COSMIC: COSV59086309;