ENST00000562058.5:n.1661A>G

Variant names:

• chr16-28605807-T-C
• rs6839
• ENST00000562058.5:n.1661A>G

Variant summary

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

The ENST00000562058.5(ENSG00000289755):​n.1661A>G variant causes a non coding transcript exon 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: ENSG00000289755 ENST00000562058.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 40 publications found

Genes affected

ENSG00000289755 (HGNC:):

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SULT1A1	NM_001055.4	c.*14A>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000314752.12	NP_001046.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1A1	ENST00000314752.12	c.*14A>G		3_prime_UTR_variant	Exon 8 of 8	1	NM_001055.4	ENSP00000321988.7

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

GnomAD2 exomes AF: 0.311 AC: 77013 AN: 247864 AF XY: 0.305

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 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

African (AFR) AF: 0.221 AC: 7303 AN: 33088

American (AMR) AF: 0.385 AC: 17069 AN: 44284

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 6432 AN: 25952

East Asian (EAS) AF: 0.101 AC: 3986 AN: 39444

South Asian (SAS) AF: 0.206 AC: 17575 AN: 85370

European-Finnish (FIN) AF: 0.450 AC: 23939 AN: 53182

Middle Eastern (MID) AF: 0.185 AC: 761 AN: 4106

European-Non Finnish (NFE) AF: 0.356 AC: 392287 AN: 1101032

Other (OTH) AF: 0.307 AC: 18333 AN: 59702

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

African (AFR) AF: 0.224 AC: 9167 AN: 40982

American (AMR) AF: 0.323 AC: 4880 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 851 AN: 3432

East Asian (EAS) AF: 0.0747 AC: 383 AN: 5126

South Asian (SAS) AF: 0.203 AC: 966 AN: 4756

European-Finnish (FIN) AF: 0.456 AC: 4753 AN: 10428

Middle Eastern (MID) AF: 0.175 AC: 50 AN: 286

European-Non Finnish (NFE) AF: 0.352 AC: 23689 AN: 67236

Other (OTH) AF: 0.265 AC: 547 AN: 2068

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
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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