rs3775775

Variant names:

• chr4-69852564-A-G
• rs3775775
• NM_005420.3:c.369+1653T>C

Variant summary

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

The NM_005420.3(SULT1E1):​c.369+1653T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,132 control chromosomes in the GnomAD database, including 1,607 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 0.13 (1607 hom., cov: 32)
• Consequence: SULT1E1 NM_005420.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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.369+1653T>C		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.369+1653T>C		intron	N/A	ENSP00000226444.3	P49888
	SULT1E1	ENST00000504002.1	TSL:1	n.475+1653T>C		intron	N/A
	SULT1E1	ENST00000904222.1		c.417+270T>C		intron	N/A	ENSP00000574281.1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19844 AN: 152014 Hom.: 1605 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.131 AC: 19866 AN: 152132 Hom.: 1607 Cov.: 32 AF XY: 0.130 AC XY: 9697 AN XY: 74386

African (AFR) AF: 0.222 AC: 9195 AN: 41474

American (AMR) AF: 0.102 AC: 1564 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3472

East Asian (EAS) AF: 0.0610 AC: 316 AN: 5184

South Asian (SAS) AF: 0.105 AC: 506 AN: 4828

European-Finnish (FIN) AF: 0.0930 AC: 986 AN: 10602

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

European-Non Finnish (NFE) AF: 0.0941 AC: 6397 AN: 67982

Other (OTH) AF: 0.150 AC: 317 AN: 2108

Alfa AF: 0.105 Hom.: 1835

Bravo AF: 0.133

Asia WGS AF: 0.103 AC: 358 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.66
PhyloP100		-0.89
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: rs3775775; hg19: chr4-70718282;