rs6639786

Positions:

• chrX-7243434-T-C

Variant summary

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

The NM_001320752.2(STS):​c.-4-9762T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 110,874 control chromosomes in the GnomAD database, including 5,281 homozygotes. There are 11,426 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 0.36 (5281 hom., 11426 hem., cov: 22)
• Consequence: STS NM_001320752.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STS	NM_001320752.2	c.-4-9762T>C		intron_variant		ENST00000674429.1
STS	NM_000351.7	c.-4-9762T>C		intron_variant
STS	NM_001320750.3	c.33-9762T>C		intron_variant
STS	NM_001320751.2	c.33-9762T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STS	ENST00000674429.1	c.-4-9762T>C		intron_variant			NM_001320752.2	P1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 39741 AN: 110822 Hom.: 5281 Cov.: 22 AF XY: 0.346 AC XY: 11428 AN XY: 33048

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.358 AC: 39735 AN: 110874 Hom.: 5281 Cov.: 22 AF XY: 0.345 AC XY: 11426 AN XY: 33110

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.372

Alfa AF: 0.367 Hom.: 4166

Bravo AF: 0.362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.65

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: rs6639786; hg19: chrX-7161475;