rs923644

Variant names:

• chrX-7643222-G-A
• rs923644
• ENST00000664306.2:n.*83+56895G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-7643222-G-A
• chrX-7643222-G-C

Variant summary

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

The ENST00000664306.2(STS):​n.*83+56895G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0401 in 110,399 control chromosomes in the GnomAD database, including 180 homozygotes. There are 1,233 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 0.040 (180 hom., 1233 hem., cov: 22)
• Consequence: STS ENST00000664306.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STS	ENST00000664306.2	n.*83+56895G>A		intron_variant	Intron 11 of 12			ENSP00000499549.2

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 4412 AN: 110343 Hom.: 176 Cov.: 22 AF XY: 0.0377 AC XY: 1230 AN XY: 32593

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0534

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0678

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0401 AC: 4424 AN: 110399 Hom.: 180 Cov.: 22 AF XY: 0.0378 AC XY: 1233 AN XY: 32659

Gnomad4 AFR AF: 0.0675

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0534

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.0131

Gnomad4 OTH AF: 0.0561

Alfa AF: 0.00873 Hom.: 35

Bravo AF: 0.0464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs923644; hg19: chrX-7561263;