rs3775768

Positions:

• chr4-69859394-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005420.3(SULT1E1):​c.-10+655G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,958 control chromosomes in the GnomAD database, including 4,307 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 0.22 (4307 hom., cov: 32)
• Consequence: SULT1E1 NM_005420.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

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]

SULT1E1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1E1	NM_005420.3	c.-10+655G>A		intron_variant		ENST00000226444.4	NP_005411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1E1	ENST00000226444.4	c.-10+655G>A		intron_variant		1	NM_005420.3	ENSP00000226444.3
SULT1E1	ENST00000504002.1	n.97+655G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33584 AN: 151840 Hom.: 4304 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.221 AC: 33596 AN: 151958 Hom.: 4307 Cov.: 32 AF XY: 0.215 AC XY: 15997 AN XY: 74272

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.241

Alfa AF: 0.278 Hom.: 7837

Bravo AF: 0.220

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.35

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

Publications

LitVar

Other links and lift over

dbSNP: rs3775768; hg19: chr4-70725112;