rs4149525

Variant names:

• chr4-69860681-T-C
• rs4149525
• ENST00000904213.1:c.-113+64A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-69860681-T-C
• chr4-69860681-T-G

Variant summary

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

The ENST00000904213.1(SULT1E1):​c.-113+64A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,022 control chromosomes in the GnomAD database, including 2,996 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 0.19 (2996 hom., cov: 31)
• Consequence: SULT1E1 ENST00000904213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 7 publications found

Genes affected

SULT1E1 (HGNC:11377): (sulfotransferase family 1E 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 a protein that transfers a sulfo moiety to and from estrone, which may control levels of estrogen receptors. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000904213.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1E1	ENST00000904213.1		c.-113+64A>G		intron	N/A	ENSP00000574272.1
	SULT1E1	ENST00000904214.1		c.-10+226A>G		intron	N/A	ENSP00000574273.1
	SULT1E1	ENST00000904215.1		c.-113+64A>G		intron	N/A	ENSP00000574274.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28622 AN: 151904 Hom.: 2985 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.169

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.189 AC: 28672 AN: 152022 Hom.: 2996 Cov.: 31 AF XY: 0.196 AC XY: 14587 AN XY: 74316

African (AFR) AF: 0.253 AC: 10470 AN: 41448

American (AMR) AF: 0.176 AC: 2692 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3466

East Asian (EAS) AF: 0.274 AC: 1413 AN: 5164

South Asian (SAS) AF: 0.194 AC: 936 AN: 4826

European-Finnish (FIN) AF: 0.264 AC: 2786 AN: 10570

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9493 AN: 67958

Other (OTH) AF: 0.165 AC: 349 AN: 2116

Alfa AF: 0.152 Hom.: 3771

Bravo AF: 0.186

Asia WGS AF: 0.209 AC: 724 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		0.040

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4149525; hg19: chr4-70726399;