rs3775768

Variant names:

• chr4-69859394-C-T
• rs3775768
• NM_005420.3:c.-10+655G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005420.3. 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
	SULT1E1	NM_005420.3	MANE Select	c.-10+655G>A		intron	N/A	NP_005411.1	Q53X91

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1E1	ENST00000226444.4	TSL:1 MANE Select	c.-10+655G>A		intron	N/A	ENSP00000226444.3	P49888
	SULT1E1	ENST00000504002.1	TSL:1	n.97+655G>A		intron	N/A
	SULT1E1	ENST00000904220.1		c.-1750G>A		5_prime_UTR	Exon 1 of 7	ENSP00000574279.1

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

African (AFR) AF: 0.106 AC: 4382 AN: 41486

American (AMR) AF: 0.245 AC: 3729 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3470

East Asian (EAS) AF: 0.183 AC: 947 AN: 5168

South Asian (SAS) AF: 0.206 AC: 992 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1932 AN: 10574

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19698 AN: 67874

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.271 Hom.: 9584

Bravo AF: 0.220

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-0.61
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: rs3775768; hg19: chr4-70725112;