chrX-149482521-TA-T

Position:

• chrX-149482521-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000202.8(IDS):​c.*224del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.36 (5392 hom., 10708 hem., cov: 7)
  • Exomes 𝑓: 0.37 (15497 hom. 28881 hem.)
• Consequence: IDS NM_000202.8 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.135

Genes affected

IDS (HGNC:5389): (iduronate 2-sulfatase) This gene encodes a member of the sulfatase family of proteins. The encoded preproprotein is proteolytically processed to generate two polypeptide chains. This enzyme is involved in the lysosomal degradation of heparan sulfate and dermatan sulfate. Mutations in this gene are associated with the X-linked lysosomal storage disease mucopolysaccharidosis type II, also known as Hunter syndrome. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-149482521-TA-T is Benign according to our data. Variant chrX-149482521-TA-T is described in ClinVar as [Benign]. Clinvar id is 1286955.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IDS	NM_000202.8	c.*224del		3_prime_UTR_variant	9/9	ENST00000340855.11
IDS	NM_001166550.4	c.*224del		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IDS	ENST00000340855.11	c.*224del		3_prime_UTR_variant	9/9	1	NM_000202.8	P1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 38475 AN: 107491 Hom.: 5394 Cov.: 7 AF XY: 0.351 AC XY: 10705 AN XY: 30523

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.498

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.373 AC: 112640 AN: 302191 Hom.: 15497 Cov.: 0 AF XY: 0.336 AC XY: 28881 AN XY: 86025

Gnomad4 AFR exome AF: 0.271

Gnomad4 AMR exome AF: 0.229

Gnomad4 ASJ exome AF: 0.347

Gnomad4 EAS exome AF: 0.135

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.420

Gnomad4 NFE exome AF: 0.428

Gnomad4 OTH exome AF: 0.372

GnomAD4 genome AF: 0.358 AC: 38466 AN: 107525 Hom.: 5392 Cov.: 7 AF XY: 0.350 AC XY: 10708 AN XY: 30569

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.363

Bravo AF: 0.340

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 22, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs71753099; hg19: chrX-148564052;