rs1881668

Variant names:

• chr4-69859738-G-C
• rs1881668
• NM_005420.3:c.-10+311C>G

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+311C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,912 control chromosomes in the GnomAD database, including 32,357 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 0.64 (32357 hom., cov: 32)
• Consequence: SULT1E1 NM_005420.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 13 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1E1	NM_005420.3	c.-10+311C>G		intron_variant	Intron 1 of 7	ENST00000226444.4	NP_005411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1E1	ENST00000226444.4	c.-10+311C>G		intron_variant	Intron 1 of 7	1	NM_005420.3	ENSP00000226444.3
SULT1E1	ENST00000504002.1	n.97+311C>G		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97560 AN: 151794 Hom.: 32345 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.643 AC: 97620 AN: 151912 Hom.: 32357 Cov.: 32 AF XY: 0.640 AC XY: 47499 AN XY: 74262

African (AFR) AF: 0.483 AC: 20008 AN: 41436

American (AMR) AF: 0.707 AC: 10788 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2334 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2852 AN: 5162

South Asian (SAS) AF: 0.758 AC: 3659 AN: 4830

European-Finnish (FIN) AF: 0.622 AC: 6569 AN: 10558

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49199 AN: 67878

Other (OTH) AF: 0.626 AC: 1319 AN: 2108

Alfa AF: 0.685 Hom.: 4510

Bravo AF: 0.640

Asia WGS AF: 0.666 AC: 2310 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.12
PromoterAI		-0.0082	Neutral
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: rs1881668; hg19: chr4-70725456;