rs2270112

Positions:

• chrX-7252884-C-G
• chrX-7252884-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001320752.2(STS):​c.-4-312C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.69 (18761 hom., 22524 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: STS NM_001320752.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.07

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 -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BP6: Variant X-7252884-C-G is Benign according to our data. Variant chrX-7252884-C-G is described in ClinVar as [Benign]. Clinvar id is 1265834.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STS	NM_001320752.2	c.-4-312C>G		intron_variant		ENST00000674429.1	NP_001307681.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STS	ENST00000674429.1	c.-4-312C>G		intron_variant			NM_001320752.2	ENSP00000501534	P1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 76217 AN: 110250 Hom.: 18759 Cov.: 22 AF XY: 0.692 AC XY: 22476 AN XY: 32476

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.552

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.688

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.691 AC: 76263 AN: 110308 Hom.: 18761 Cov.: 22 AF XY: 0.692 AC XY: 22524 AN XY: 32544

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.689

Alfa AF: 0.468 Hom.: 1823

Bravo AF: 0.705

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.32

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: rs2270112; hg19: chrX-7170925;