NM_001055.4:c.-5+452G>C

Variant names:

• chr16-28609479-C-G
• rs3760091
• NM_001055.4:c.-5+452G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001055.4(SULT1A1):​c.-5+452G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 1,141,004 control chromosomes in the GnomAD database, including 80,245 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 0.38 (9428 hom., cov: 37)
  • Exomes 𝑓: 0.40 (70817 hom.)
• Consequence: SULT1A1 NM_001055.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• 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=-1.09).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001055.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1A1	NM_001055.4	MANE Select	c.-5+452G>C		intron	N/A	NP_001046.2
	SULT1A1	NM_001394422.1		c.-425G>C		5_prime_UTR_premature_start_codon_gain	Exon 3 of 10	NP_001381351.1	P50225-1
	SULT1A1	NM_177530.4		c.-425G>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 8	NP_803566.1	P50225-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1A1	ENST00000314752.12	TSL:1 MANE Select	c.-5+452G>C		intron	N/A	ENSP00000321988.7	P50225-1
	ENSG00000289755	ENST00000562058.5	TSL:1	n.755+452G>C		intron	N/A
	ENSG00000289755	ENST00000564818.5	TSL:1	n.455-44G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57251 AN: 150576 Hom.: 9420 Cov.: 37

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.404

GnomAD2 exomes AF: 0.378 AC: 48484 AN: 128248 AF XY: 0.376

Gnomad AFR exome AF: 0.342

Gnomad AMR exome AF: 0.380

Gnomad ASJ exome AF: 0.399

Gnomad EAS exome AF: 0.341

Gnomad FIN exome AF: 0.434

Gnomad NFE exome AF: 0.400

Gnomad OTH exome AF: 0.412

GnomAD4 exome AF: 0.397 AC: 393604 AN: 990310 Hom.: 70817 Cov.: 15 AF XY: 0.394 AC XY: 193413 AN XY: 490840

African (AFR) AF: 0.358 AC: 8051 AN: 22458

American (AMR) AF: 0.375 AC: 10159 AN: 27080

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 5931 AN: 14636

East Asian (EAS) AF: 0.349 AC: 4187 AN: 11986

South Asian (SAS) AF: 0.326 AC: 23593 AN: 72412

European-Finnish (FIN) AF: 0.439 AC: 5618 AN: 12790

Middle Eastern (MID) AF: 0.466 AC: 1916 AN: 4108

European-Non Finnish (NFE) AF: 0.405 AC: 319489 AN: 788178

Other (OTH) AF: 0.400 AC: 14660 AN: 36662

GnomAD4 genome AF: 0.380 AC: 57290 AN: 150694 Hom.: 9428 Cov.: 37 AF XY: 0.380 AC XY: 28000 AN XY: 73588

African (AFR) AF: 0.347 AC: 14229 AN: 40948

American (AMR) AF: 0.374 AC: 5664 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3460

East Asian (EAS) AF: 0.362 AC: 1809 AN: 4998

South Asian (SAS) AF: 0.314 AC: 1500 AN: 4772

European-Finnish (FIN) AF: 0.431 AC: 4530 AN: 10500

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.396 AC: 26739 AN: 67600

Other (OTH) AF: 0.405 AC: 840 AN: 2074

Alfa AF: 0.385 Hom.: 1709

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.054
DANN	Benign	0.28
PhyloP100		-1.5
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: rs3760091; hg19: chr16-28620800; COSMIC: COSV59086574; COSMIC: COSV59086574;