rs1881668

Positions:

• chr4-69859738-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• 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/exons	MANE	UniProt
SULT1E1	NM_005420.3	c.-10+311C>G		intron_variant		ENST00000226444.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT1E1	ENST00000226444.4	c.-10+311C>G		intron_variant		1	NM_005420.3	P1
SULT1E1	ENST00000504002.1	n.97+311C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.626

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

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: rs1881668; hg19: chr4-70725456;