chr16-28605736-G-A

Variant names:

• chr16-28605736-G-A
• rs1042157
• ENST00000562058.5:n.1732C>T

Variant summary

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

The ENST00000562058.5(ENSG00000289755):​n.1732C>T 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 0.372 in 1,576,354 control chromosomes in the GnomAD database, including 108,856 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 (9039 hom., cov: 36)
  • Exomes 𝑓: 0.38 (99817 hom.)
• Consequence: ENSG00000289755 ENST00000562058.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 35 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562058.5. 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.*85C>T		3_prime_UTR	Exon 8 of 8	NP_001046.2
	SULT1A1	NM_001394421.1		c.*85C>T		3_prime_UTR	Exon 11 of 11	NP_001381350.1
	SULT1A1	NM_001394422.1		c.*85C>T		3_prime_UTR	Exon 10 of 10	NP_001381351.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289755	ENST00000562058.5	TSL:1	n.1732C>T		non_coding_transcript_exon	Exon 10 of 10
	ENSG00000289755	ENST00000564818.5	TSL:1	n.1504C>T		non_coding_transcript_exon	Exon 11 of 11
	SULT1A1	ENST00000314752.12	TSL:1 MANE Select	c.*85C>T		3_prime_UTR	Exon 8 of 8	ENSP00000321988.7

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51215 AN: 150042 Hom.: 9030 Cov.: 36

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.314

GnomAD4 exome AF: 0.375 AC: 535444 AN: 1426204 Hom.: 99817 Cov.: 33 AF XY: 0.372 AC XY: 263556 AN XY: 708640

African (AFR) AF: 0.230 AC: 7550 AN: 32760

American (AMR) AF: 0.479 AC: 19828 AN: 41378

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 7619 AN: 25542

East Asian (EAS) AF: 0.215 AC: 8131 AN: 37898

South Asian (SAS) AF: 0.241 AC: 20129 AN: 83592

European-Finnish (FIN) AF: 0.462 AC: 24123 AN: 52188

Middle Eastern (MID) AF: 0.232 AC: 942 AN: 4058

European-Non Finnish (NFE) AF: 0.391 AC: 426512 AN: 1089958

Other (OTH) AF: 0.350 AC: 20610 AN: 58830

GnomAD4 genome AF: 0.341 AC: 51263 AN: 150150 Hom.: 9039 Cov.: 36 AF XY: 0.343 AC XY: 25147 AN XY: 73340

African (AFR) AF: 0.237 AC: 9735 AN: 40990

American (AMR) AF: 0.404 AC: 6094 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1032 AN: 3438

East Asian (EAS) AF: 0.239 AC: 1182 AN: 4950

South Asian (SAS) AF: 0.231 AC: 1098 AN: 4752

European-Finnish (FIN) AF: 0.469 AC: 4901 AN: 10440

Middle Eastern (MID) AF: 0.210 AC: 60 AN: 286

European-Non Finnish (NFE) AF: 0.391 AC: 26327 AN: 67254

Other (OTH) AF: 0.314 AC: 646 AN: 2058

Alfa AF: 0.364 Hom.: 6955

Asia WGS AF: 0.284 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.82
PhyloP100		-0.049
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1042157; hg19: chr16-28617057; COSMIC: COSV59087578; COSMIC: COSV59087578;