rs6848974
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000203.5(IDUA):c.590-8C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000487 in 1,601,556 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000203.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDUA | NM_000203.5 | c.590-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000514224.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDUA | ENST00000514224.2 | c.590-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_000203.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152066Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000137 AC: 32AN: 233562Hom.: 1 AF XY: 0.000141 AC XY: 18AN XY: 127814
GnomAD4 exome AF: 0.0000442 AC: 64AN: 1449372Hom.: 1 Cov.: 34 AF XY: 0.0000402 AC XY: 29AN XY: 721214
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74416
ClinVar
Submissions by phenotype
Mucopolysaccharidosis type 1 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at