rs1131289

Positions:

• chrX-7352955-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001320752.2(STS):​c.*2694A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.66 (16708 hom., 20406 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: STS NM_001320752.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

STS (HGNC:11425): (steroid sulfatase) This gene encodes a multi-pass membrane protein that is localized to the endoplasmic reticulum. It belongs to the sulfatase family and hydrolyzes several 3-beta-hydroxysteroid sulfates, which serve as metabolic precursors for estrogens, androgens, and cholesterol. Mutations in this gene are associated with X-linked ichthyosis (XLI). Alternatively spliced transcript variants resulting from the use of different promoters have been described for this gene (PMID:17601726). [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STS	NM_001320752.2	c.*2694A>G		3_prime_UTR_variant	11/11	ENST00000674429.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STS	ENST00000674429.1	c.*2694A>G		3_prime_UTR_variant	11/11		NM_001320752.2	P1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 70875 AN: 108158 Hom.: 16714 Cov.: 22 AF XY: 0.659 AC XY: 20390 AN XY: 30930

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.833

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.670

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 Data not reliable, filtered out with message: InbreedingCoeff AF: 0.655 AC: 70877 AN: 108203 Hom.: 16708 Cov.: 22 AF XY: 0.659 AC XY: 20406 AN XY: 30987

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.674

Alfa AF: 0.616 Hom.: 10897

Bravo AF: 0.632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.28
DANN	Benign	0.57

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: rs1131289; hg19: chrX-7270996;