rs1000900

chrX-7234072-G-AchrX-7234072-G-C

Variant summary

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

The NM_001320752.2(STS):c.-4-19124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 111,060 control chromosomes in the GnomAD database, including 2,521 homozygotes. There are 7,922 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 0.23 (2521 hom., 7922 hem., cov: 23)
• Consequence: STS NM_001320752.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STS	NM_001320752.2	c.-4-19124G>A		intron_variant		ENST00000674429.1
STS	NM_000351.7	c.-5+14386G>A		intron_variant
STS	NM_001320750.3	c.33-19124G>A		intron_variant
STS	NM_001320751.2	c.33-19124G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STS	ENST00000674429.1	c.-4-19124G>A		intron_variant			NM_001320752.2	P1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 25995 AN: 111007 Hom.: 2523 Cov.: 23 AF XY: 0.238 AC XY: 7909 AN XY: 33281

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0767

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.234 AC: 26002 AN: 111060 Hom.: 2521 Cov.: 23 AF XY: 0.238 AC XY: 7922 AN XY: 33344

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.238

Alfa AF: 0.252 Hom.: 9765

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.89
Dann	Benign	0.17

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: rs1000900; hg19: chrX-7152113;