rs3775779

Variant names:

• chr4-69843489-T-A
• rs3775779
• NM_005420.3:c.772+672A>T

Variant summary

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

The NM_005420.3(SULT1E1):​c.772+672A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,052 control chromosomes in the GnomAD database, including 6,010 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 0.27 (6010 hom., cov: 32)
• Consequence: SULT1E1 NM_005420.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 10 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]

ENSG00000284695 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1E1	NM_005420.3	c.772+672A>T		intron_variant	Intron 7 of 7	ENST00000226444.4	NP_005411.1
SULT1E1	XM_047416100.1	c.772+672A>T		intron_variant	Intron 6 of 6		XP_047272056.1
SULT1E1	XM_047416101.1	c.772+672A>T		intron_variant	Intron 7 of 7		XP_047272057.1
SULT1E1	XR_007057952.1	n.878+672A>T		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1E1	ENST00000226444.4	c.772+672A>T		intron_variant	Intron 7 of 7	1	NM_005420.3	ENSP00000226444.3
ENSG00000284695	ENST00000506796.5	n.268+672A>T		intron_variant	Intron 2 of 5	5		ENSP00000420891.1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40514 AN: 151936 Hom.: 6015 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.266 AC: 40505 AN: 152052 Hom.: 6010 Cov.: 32 AF XY: 0.269 AC XY: 19989 AN XY: 74318

African (AFR) AF: 0.141 AC: 5831 AN: 41482

American (AMR) AF: 0.335 AC: 5115 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1147 AN: 5154

South Asian (SAS) AF: 0.431 AC: 2076 AN: 4814

European-Finnish (FIN) AF: 0.293 AC: 3090 AN: 10564

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21311 AN: 67966

Other (OTH) AF: 0.259 AC: 546 AN: 2108

Alfa AF: 0.293 Hom.: 998

Bravo AF: 0.260

Asia WGS AF: 0.285 AC: 992 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		0.16
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: rs3775779; hg19: chr4-70709207;