Variant X-7148010-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001320752.2(STS):c.-207A>C variant causes a 5 prime UTR 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 0.68 ( 18532 hom., 21106 hem., cov: 21)

Exomes 𝑓: 0.61 ( 124680 hom. 180816 hem. )

Failed GnomAD Quality Control

Consequence

STS
NM_001320752.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0340

Variant links:

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 links:

PUDP (HGNC:16818): (pseudouridine 5'-phosphatase) This gene encodes a member of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The encoded protein has no known biological function. This gene has a pseudogene on chromosome 1. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]

PUDP links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STS	NM_001320752.2 linkuse as main transcript	c.-207A>C		5_prime_UTR_variant	1/11	ENST00000674429.1
PUDP	NM_012080.5 linkuse as main transcript	c.61+43T>G		intron_variant		ENST00000381077.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STS	ENST00000674429.1 linkuse as main transcript	c.-207A>C		5_prime_UTR_variant	1/11		NM_001320752.2	P1
PUDP	ENST00000381077.10 linkuse as main transcript	c.61+43T>G		intron_variant		1	NM_012080.5	P1	Q08623-1

Frequencies

GnomAD3 genomes

AF:

0.677

AC:

73652

AN:

108741

Hom.:

18530

Cov.:

AF XY:

0.671

AC XY:

21053

AN XY:

31359

show subpopulations

Gnomad AFR

AF:

0.868

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.669

Gnomad ASJ

AF:

0.634

Gnomad EAS

AF:

0.593

Gnomad SAS

AF:

0.753

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.632

Gnomad NFE

AF:

0.592

Gnomad OTH

AF:

0.654

GnomAD3 exomes

AF:

0.624

AC:

54692

AN:

87580

Hom.:

11594

AF XY:

0.635

AC XY:

18206

AN XY:

28688

show subpopulations

Gnomad AFR exome

AF:

0.878

Gnomad AMR exome

AF:

0.636

Gnomad ASJ exome

AF:

0.626

Gnomad EAS exome

AF:

0.559

Gnomad SAS exome

AF:

0.761

Gnomad FIN exome

AF:

0.548

Gnomad NFE exome

AF:

0.583

Gnomad OTH exome

AF:

0.628

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.609

AC:

588589

AN:

966760

Hom.:

124680

Cov.:

AF XY:

0.622

AC XY:

180816

AN XY:

290862

show subpopulations

Gnomad4 AFR exome

AF:

0.878

Gnomad4 AMR exome

AF:

0.643

Gnomad4 ASJ exome

AF:

0.634

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.758

Gnomad4 FIN exome

AF:

0.546

Gnomad4 NFE exome

AF:

0.592

Gnomad4 OTH exome

AF:

0.617

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.678

AC:

73702

AN:

108781

Hom.:

18532

Cov.:

AF XY:

0.672

AC XY:

21106

AN XY:

31409

show subpopulations

Gnomad4 AFR

AF:

0.868

Gnomad4 AMR

AF:

0.669

Gnomad4 ASJ

AF:

0.634

Gnomad4 EAS

AF:

0.592

Gnomad4 SAS

AF:

0.754

Gnomad4 FIN

AF:

0.537

Gnomad4 NFE

AF:

0.592

Gnomad4 OTH

AF:

0.650

Alfa

AF:

0.637

Hom.:

14679

Bravo

AF:

0.690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

9.0

DANN

Benign

0.30

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over