4-1002713-G-GC
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000203.5(IDUA):c.1190-10dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 149,514 control chromosomes in the GnomAD database, including 2,046 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.16 ( 2046 hom., cov: 29)
Exomes 𝑓: 0.093 ( 3064 hom. )
Failed GnomAD Quality Control
Consequence
IDUA
NM_000203.5 intron
NM_000203.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.792
Genes affected
IDUA (HGNC:5391): (alpha-L-iduronidase) This gene encodes an enzyme that hydrolyzes the terminal alpha-L-iduronic acid residues of two glycosaminoglycans, dermatan sulfate and heparan sulfate. This hydrolysis is required for the lysosomal degradation of these glycosaminoglycans. Mutations in this gene that result in enzymatic deficiency lead to the autosomal recessive disease mucopolysaccharidosis type I (MPS I). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 4-1002713-G-GC is Benign according to our data. Variant chr4-1002713-G-GC is described in ClinVar as [Benign]. Clinvar id is 92626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDUA | NM_000203.5 | c.1190-10dup | intron_variant | ENST00000514224.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDUA | ENST00000514224.2 | c.1190-10dup | intron_variant | 2 | NM_000203.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.164 AC: 24511AN: 149414Hom.: 2051 Cov.: 29
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GnomAD3 exomes AF: 0.160 AC: 11726AN: 73188Hom.: 595 AF XY: 0.174 AC XY: 7220AN XY: 41468
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0927 AC: 110358AN: 1190586Hom.: 3064 Cov.: 24 AF XY: 0.0998 AC XY: 58876AN XY: 590056
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.164 AC: 24506AN: 149514Hom.: 2046 Cov.: 29 AF XY: 0.164 AC XY: 11960AN XY: 72964
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ClinVar
Significance: Benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 17, 2012 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 17, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jan 15, 2016 | Variant summary: The c.1190-10dupC variant affects a intronic polyC site. One in-silico tool predicts benign outcome for this variant. 5/5 programs in Alamut predict that this variant does not affect normal splicing. This variant is found in 1655/7502 control chromosomes (116 homozygotes) at a frequency of 0.2206078, which is about 82 times of maximal expected frequency of a pathogenic allele (0.0026926), suggesting this variant is benign. In addition, one clinical laboratory classified this variant as bengin. Taken together, this variant was classified as benign. - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 02, 2016 | - - |
Mucopolysaccharidosis type 1 Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at