rs3775779

chr4-69843489-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SULT1E1	NM_005420.3	c.772+672A>T		intron_variant		ENST00000226444.4
SULT1E1	XM_047416100.1	c.772+672A>T		intron_variant
SULT1E1	XM_047416101.1	c.772+672A>T		intron_variant
SULT1E1	XR_007057952.1	n.878+672A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT1E1	ENST00000226444.4	c.772+672A>T		intron_variant		1	NM_005420.3	P1

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

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.259

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

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: rs3775779; hg19: chr4-70709207;