X-7197052-A-T

Variant names:

• chrX-7197052-A-T
• rs707762
• NM_001320752.2:c.-5+6044A>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001320752.2(STS):​c.-5+6044A>T variant causes a intron 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 0.63 (15318 hom., 19285 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: STS NM_001320752.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

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]

STS Gene-Disease associations (from GenCC):

• recessive X-linked ichthyosis

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STS	NM_001320752.2	c.-5+6044A>T		intron_variant	Intron 2 of 10	ENST00000674429.1	NP_001307681.2
STS	NM_001320750.3	c.32+6044A>T		intron_variant	Intron 2 of 10		NP_001307679.1
STS	NM_001320751.2	c.32+6044A>T		intron_variant	Intron 3 of 11		NP_001307680.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STS	ENST00000674429.1	c.-5+6044A>T		intron_variant	Intron 2 of 10		NM_001320752.2	ENSP00000501534.1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 67803 AN: 108378 Hom.: 15318 Cov.: 21

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.616

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.613

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: 0.626 AC: 67864 AN: 108432 Hom.: 15318 Cov.: 21 AF XY: 0.626 AC XY: 19285 AN XY: 30824

African (AFR) AF: 0.692 AC: 20555 AN: 29710

American (AMR) AF: 0.649 AC: 6595 AN: 10163

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 1662 AN: 2603

East Asian (EAS) AF: 0.599 AC: 2016 AN: 3363

South Asian (SAS) AF: 0.749 AC: 1844 AN: 2462

European-Finnish (FIN) AF: 0.540 AC: 3003 AN: 5558

Middle Eastern (MID) AF: 0.627 AC: 133 AN: 212

European-Non Finnish (NFE) AF: 0.592 AC: 30908 AN: 52210

Other (OTH) AF: 0.610 AC: 905 AN: 1483

Alfa AF: 0.352 Hom.: 1193

Bravo AF: 0.630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs707762; hg19: chrX-7115093;