rs4788068

Variant names:

• chr16-28605402-C-T
• rs4788068
• NM_001055.4:c.*419G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.394 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1A1	NM_001055.4	MANE Select	c.*419G>A		3_prime_UTR	Exon 8 of 8	NP_001046.2
	SULT1A1	NM_001394421.1		c.*419G>A		3_prime_UTR	Exon 11 of 11	NP_001381350.1
	SULT1A1	NM_001394422.1		c.*419G>A		3_prime_UTR	Exon 10 of 10	NP_001381351.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1A1	ENST00000314752.12	TSL:1 MANE Select	c.*419G>A		3_prime_UTR	Exon 8 of 8	ENSP00000321988.7
	SULT1A1	ENST00000569554.5	TSL:1	c.*419G>A		3_prime_UTR	Exon 7 of 7	ENSP00000457912.1
	SULT1A1	ENST00000898554.1		c.*419G>A		3_prime_UTR	Exon 9 of 9	ENSP00000568613.1

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

African (AFR) AF: 0.191 AC: 718 AN: 3766

American (AMR) AF: 0.409 AC: 1804 AN: 4414

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 951 AN: 3388

East Asian (EAS) AF: 0.233 AC: 1218 AN: 5222

South Asian (SAS) AF: 0.224 AC: 5779 AN: 25780

European-Finnish (FIN) AF: 0.428 AC: 2574 AN: 6008

Middle Eastern (MID) AF: 0.206 AC: 110 AN: 534

European-Non Finnish (NFE) AF: 0.365 AC: 28809 AN: 78902

Other (OTH) AF: 0.343 AC: 2245 AN: 6542

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

African (AFR) AF: 0.237 AC: 9696 AN: 40962

American (AMR) AF: 0.403 AC: 6044 AN: 15016

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1028 AN: 3434

East Asian (EAS) AF: 0.239 AC: 1186 AN: 4972

South Asian (SAS) AF: 0.227 AC: 1073 AN: 4734

European-Finnish (FIN) AF: 0.468 AC: 4873 AN: 10410

Middle Eastern (MID) AF: 0.219 AC: 63 AN: 288

European-Non Finnish (NFE) AF: 0.391 AC: 26327 AN: 67294

Other (OTH) AF: 0.317 AC: 660 AN: 2082

Alfa AF: 0.381 Hom.: 1242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.46
PhyloP100		-3.5

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

Other links and lift over

dbSNP: rs4788068; hg19: chr16-28616723;