4-69860103-C-T

Variant names:

• chr4-69860103-C-T
• rs3736599
• ENST00000504002.1:n.43G>A

Variant summary

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

The ENST00000504002.1(SULT1E1):​n.43G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 151,792 control chromosomes in the GnomAD database, including 1,601 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 (1601 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SULT1E1 ENST00000504002.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 32 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1E1	NM_005420.3	c.-64G>A		5_prime_UTR_variant	Exon 1 of 8	ENST00000226444.4	NP_005411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1E1	ENST00000504002.1	n.43G>A		non_coding_transcript_exon_variant	Exon 1 of 5	1
SULT1E1	ENST00000226444.4	c.-64G>A		5_prime_UTR_variant	Exon 1 of 8	1	NM_005420.3	ENSP00000226444.3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20126 AN: 151674 Hom.: 1605 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.130

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.133 AC: 20153 AN: 151792 Hom.: 1601 Cov.: 32 AF XY: 0.134 AC XY: 9930 AN XY: 74180

African (AFR) AF: 0.194 AC: 8031 AN: 41400

American (AMR) AF: 0.112 AC: 1711 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1562 AN: 5158

South Asian (SAS) AF: 0.149 AC: 716 AN: 4814

European-Finnish (FIN) AF: 0.0981 AC: 1032 AN: 10524

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0957 AC: 6499 AN: 67882

Other (OTH) AF: 0.129 AC: 272 AN: 2106

Alfa AF: 0.112 Hom.: 3435

Bravo AF: 0.135

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.1
DANN	Benign	0.59
PhyloP100		0.17
PromoterAI		-0.012	Neutral
Mutation Taster		=300/0	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: rs3736599; hg19: chr4-70725821;