4-69860103-C-T

Position:

• chr4-69860103-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005420.3(SULT1E1):​c.-64G>A variant causes a 5 prime UTR 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 NM_005420.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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=-0.82).
• 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/exons	MANE	Protein	UniProt
SULT1E1	NM_005420.3	c.-64G>A		5_prime_UTR_variant	1/8	ENST00000226444.4	NP_005411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1E1	ENST00000226444.4	c.-64G>A		5_prime_UTR_variant	1/8	1	NM_005420.3	ENSP00000226444	P1
SULT1E1	ENST00000504002.1	n.43G>A		non_coding_transcript_exon_variant	1/5	1

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

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

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0981

Gnomad4 NFE AF: 0.0957

Gnomad4 OTH AF: 0.129

Alfa AF: 0.106 Hom.: 1240

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

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: rs3736599; hg19: chr4-70725821;