4-69857726-C-G

Position:

• chr4-69857726-C-G

Variant summary

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

The NM_005420.3(SULT1E1):​c.-9-73G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 1,417,968 control chromosomes in the GnomAD database, including 82,192 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 0.30 (7168 hom., cov: 32)
  • Exomes 𝑓: 0.34 (75024 hom.)
• Consequence: SULT1E1 NM_005420.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1E1	NM_005420.3	c.-9-73G>C		intron_variant		ENST00000226444.4	NP_005411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1E1	ENST00000226444.4	c.-9-73G>C		intron_variant		1	NM_005420.3	ENSP00000226444	P1
SULT1E1	ENST00000504002.1	n.98-73G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45581 AN: 151834 Hom.: 7164 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.299

GnomAD4 exome AF: 0.343 AC: 434271 AN: 1266016 Hom.: 75024 AF XY: 0.341 AC XY: 213315 AN XY: 625248

Gnomad4 AFR exome AF: 0.234

Gnomad4 AMR exome AF: 0.261

Gnomad4 ASJ exome AF: 0.345

Gnomad4 EAS exome AF: 0.270

Gnomad4 SAS exome AF: 0.268

Gnomad4 FIN exome AF: 0.259

Gnomad4 NFE exome AF: 0.360

Gnomad4 OTH exome AF: 0.329

GnomAD4 genome AF: 0.300 AC: 45605 AN: 151952 Hom.: 7168 Cov.: 32 AF XY: 0.292 AC XY: 21703 AN XY: 74234

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.299

Alfa AF: 0.219 Hom.: 603

Bravo AF: 0.301

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.37

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: rs4149530; hg19: chr4-70723444;