16-28608363-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001055.4(SULT1A1):c.300G>A(p.Pro100=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000536 in 1,612,176 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00050 (1 hom., cov: 34)
  • Exomes 𝑓: 0.00054 (24 hom.)
• Consequence: SULT1A1 NM_001055.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.79

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 -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BP6: Variant 16-28608363-C-T is Benign according to our data. Variant chr16-28608363-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646351.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.79 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT1A1	NM_001055.4	c.300G>A	p.Pro100=	synonymous_variant	4/8	ENST00000314752.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT1A1	ENST00000314752.12	c.300G>A	p.Pro100=	synonymous_variant	4/8	1	NM_001055.4	P1
SULT1A1	ENST00000569554.5	c.300G>A	p.Pro100=	synonymous_variant	3/7	1		P1
SULT1A1	ENST00000566189.5	c.300G>A	p.Pro100=	synonymous_variant	4/8	5
SULT1A1	ENST00000567512.1	c.174G>A	p.Pro58=	synonymous_variant	3/6	3

Frequencies

GnomAD3 genomes AF: 0.000501 AC: 76 AN: 151638 Hom.: 1 Cov.: 34

Gnomad AFR AF: 0.000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000330

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000417

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000840

Gnomad OTH AF: 0.000481

GnomAD3 exomes AF: 0.000219 AC: 55 AN: 251280 Hom.: 0 AF XY: 0.000258 AC XY: 35 AN XY: 135802

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.000163

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000334

Gnomad OTH exome AF: 0.000327

GnomAD4 exome AF: 0.000540 AC: 788 AN: 1460420 Hom.: 24 Cov.: 30 AF XY: 0.000527 AC XY: 383 AN XY: 726538

Gnomad4 AFR exome AF: 0.000120

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.0000766

Gnomad4 EAS exome AF: 0.000252

Gnomad4 SAS exome AF: 0.000128

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000626

Gnomad4 OTH exome AF: 0.000945

GnomAD4 genome AF: 0.000501 AC: 76 AN: 151756 Hom.: 1 Cov.: 34 AF XY: 0.000472 AC XY: 35 AN XY: 74162

Gnomad4 AFR AF: 0.000241

Gnomad4 AMR AF: 0.000329

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.000417

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000840

Gnomad4 OTH AF: 0.000476

Alfa AF: 0.000402 Hom.: 0

EpiCase AF: 0.000601

EpiControl AF: 0.000237

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

SULT1A1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	2.0
Dann	Benign	0.38

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: rs1041986; hg19: chr16-28619684;