rs2024159

chrX-7248171-C-A

Variant summary

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

The NM_001320752.2(STS):c.-4-5025C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 111,250 control chromosomes in the GnomAD database, including 2,937 homozygotes. There are 8,743 hemizygotes in GnomAD. 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 0.26 (2937 hom., 8743 hem., cov: 23)
• Consequence: STS NM_001320752.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STS	NM_001320752.2	c.-4-5025C>A		intron_variant		ENST00000674429.1
STS	NM_000351.7	c.-4-5025C>A		intron_variant
STS	NM_001320750.3	c.33-5025C>A		intron_variant
STS	NM_001320751.2	c.33-5025C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STS	ENST00000674429.1	c.-4-5025C>A		intron_variant			NM_001320752.2	P1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 29023 AN: 111195 Hom.: 2939 Cov.: 23 AF XY: 0.261 AC XY: 8730 AN XY: 33415

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.256

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.261 AC: 29032 AN: 111250 Hom.: 2937 Cov.: 23 AF XY: 0.261 AC XY: 8743 AN XY: 33480

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.254

Alfa AF: 0.281 Hom.: 2431

Bravo AF: 0.268

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.67
Dann	Benign	0.76

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: rs2024159; hg19: chrX-7166212;