Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: SLC26A1 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: SLC26A1 CSPEC Genes: [ 'IDUA' ] * Message MONDOs: MONDO:0001586 CSPEC MONDO: [ 'MONDO:0001586' ]
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_022042.4(SLC26A1):c.*878G>A

CA145880

92640 (ClinVar)

Gene: SLC26A1
Condition: mucopolysaccharidosis type 1
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: acb35f28-4d3a-4720-a8af-a98870b776fc
Approved on: 2025-04-21
Published on: 2025-05-02

HGVS expressions

NM_022042.4:c.*878G>A
NM_022042.4(SLC26A1):c.*878G>A
NC_000004.12:g.987955C>T
CM000666.2:g.987955C>T
NC_000004.11:g.981743C>T
CM000666.1:g.981743C>T
NC_000004.10:g.971743C>T
NG_008103.1:g.5959C>T
NG_033042.1:g.10482G>A
ENST00000247933.9:c.299+6C>T
ENST00000398516.3:c.*878G>A
ENST00000514224.2:c.299+6C>T
ENST00000247933.8:c.299+6C>T
ENST00000361661.6:c.*878G>A
ENST00000398520.6:c.576+3173G>A
ENST00000502910.5:c.158+713C>T
ENST00000504568.5:c.259+44C>T
ENST00000506561.5:n.308+6C>T
ENST00000508168.5:n.177+713C>T
ENST00000509744.1:n.35+6C>T
ENST00000514698.5:n.199+713C>T
ENST00000622731.4:c.576+3173G>A
NM_000203.4:c.299+6C>T
NM_022042.3:c.*878G>A
NM_134425.2:c.576+3173G>A
NM_213613.3:c.*878G>A
NR_110313.1:n.387+6C>T
NM_000203.5:c.299+6C>T
NM_134425.3:c.576+3173G>A
NM_213613.4:c.*878G>A
NM_134425.4:c.576+3173G>A
More

Benign

Met criteria codes 1
BA1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Lysosomal Diseases Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for IDUA Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Lysosomal Diseases VCEP
The NM_000203.5:c.299+6C>T variant in IDUA alters a nucleotide in the region of the donor splice site of intron 2. The filtering allele frequency (the lower threshold of the 95% CI of 14986/1566936) of the c.299+6C>T variant in IDUA is 0.02373 in the Middle Eastern population chromosomes by gnomAD v4.1.0., which is higher than the ClinGen Lysosomal Diseases VCEP’s threshold for BA1 (>0.005), and therefore meets this criterion (BA1). There is a ClinVar entry for this variant (Variation ID: 92640). In summary, this variant meets the criteria to be classified as benign for mucopolysaccharidosis type I. IDUA-specific ACMG/AMP criteria applied, as specified by the ClinGen LD VCEP (Specifications Version 1.0.0.): BA1 (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on April 21, 2025).
Met criteria codes
BA1
The filtering allele frequency (the lower threshold of the 95% CI of 14986/1566936) of the c.299+6C>T variant in IDUA is 0.02373 in the Middle Eastern population chromosomes by gnomAD v4.1.0., which is higher than the ClinGen Lysosomal Diseases VCEP’s threshold for BA1 (>0.005), and therefore meets this criterion (BA1).
Curation History
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