NM_000110.3(DPYD):c.1905+1G>A

Variation ID: Help
432
Review status: Help
reviewed by expert panel3 stars out of maximum of 4 stars

Interpretation Help

Allele(s) Help

NM_000110.3(DPYD):c.1905+1G>A

Allele ID:
15471
Variant type:
single nucleotide variant
Cytogenetic location:
1p21.3
Genomic location:
  • Chr1: 97450058 (on Assembly GRCh38)
  • Chr1: 97915614 (on Assembly GRCh37)
  • Chr1: 97688202 (on Assembly NCBI36)
Other names:
  • IVS14, G-A, +1
HGVS:
  • NG_008807.2:g.476002G>A
  • NM_000110.3:c.1905+1G>A
  • NC_000001.11:g.97450058C>T (GRCh38)
  • LRG_722t1:c.1905+1G>A
  • NC_000001.10:g.97915614C>T (GRCh37)
  • NC_000001.9:g.97688202C>T (NCBI36)
  • LRG_722:g.476002G>A
Note:
NCBI staff reviewed the sequence information reported in PubMed 8892022 Fig. 3 to determine the location of this allele on the current reference sequence.
Links:
NCBI 1000 Genomes Browser:
rs3918290
Molecular consequence:
NM_000110.3:c.1905+1G>A: splice donor variant [Sequence Ontology SO:0001575]
Allele frequency:
  • GO-ESP 0.00415 (T)
  • GMAF 0.00300 (T)

Variant frequency in dbGaP Help

NM_000110.3(DPYD):c.1905+1G>A

GRCh37 Chr1:97915614
Called variantsPotential variants
Sample count136 of 8573352 of 40953

Called variants are samples submitted to dbGaP that have the variant allele. Potential variants are SRA runs that display the allele in at least 30% of the reads covering the position, and have 10 or more passing reads covering the position.

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Assertion and evidence details

Germline

Clinical significance
(Last evaluated)
Review status
(Assertion method)
Collection methodCondition(s)
(Mode of inheritance)
OriginCitationsSubmitter - Study nameSubmission accession
Pathogenic
(Jun 1, 2015)
criteria provided, single submitter
(EGL Classification Definitions)
clinical testing
  • Dihydropyrimidine dehydrogenase deficiency[MedGen | OMIM]
germlineEmory Genetics Laboratory,Emory UniversitySCV000225998.1
Uncertain significance
(Apr 1, 2015)
no assertion criteria providedresearchgermline
    Department of Genetics, Reproduction and Fetal Medicine.,Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville.SCV000222717.1
    Pathogenic
    (Jan 1, 1999)
    no assertion criteria providedliterature only
    • Dihydropyrimidine dehydrogenase deficiency[MedGen | OMIM]
    germlineOMIMSCV000020609.1
    not providedno assertion providedliterature onlyunknown
      Diasio Lab, Mayo ClinicSCV000118634.1

      PGx

      Clinical significance
      (Last evaluated)
      Review status
      (Assertion method)
      Collection methodCondition(s)
      (Mode of inheritance)
      OriginCitationsSubmitter - Study nameSubmission accession
      drug responsereviewed by expert panel
      (Pharmacogenomics knowledge for personalized medicine)
      literature onlyCondition: capecitabine response - Toxicity/ADR
      • Drug reported used for: Drug Toxicity[MedGen]
      • Drug reported used for: Breast Neoplasms[MedGen]
      • Drug reported used for: Neoplasms[MedGen]
      germlinePharmGKBSCV000268315.1
      drug responsereviewed by expert panel
      (Pharmacogenomics knowledge for personalized medicine)
      literature onlyCondition: fluorouracil response - Toxicity/ADR
      • Drug reported used for: Drug Toxicity[MedGen]
      • Drug reported used for: Breast Neoplasms[MedGen]
      • Drug reported used for: Neoplasms[MedGen]
      germlinePharmGKBSCV000268316.1
      drug responsereviewed by expert panel
      (Pharmacogenomics knowledge for personalized medicine)
      literature onlyCondition: Pyrimidine analogues response - Toxicity/ADR
      • Drug reported used for: Neoplasms[MedGen]
      germlinePharmGKBSCV000268317.1
      drug responsereviewed by expert panel
      (Pharmacogenomics knowledge for personalized medicine)
      literature onlyCondition: tegafur response - Toxicity/ADR
      • Drug reported used for: Drug Toxicity[MedGen]
      • Drug reported used for: Neoplasms[MedGen]
      germlinePharmGKBSCV000268318.1
      Pathogenic
      (Jan 1, 1999)
      no assertion criteria providedliterature onlyCondition: not provided
      germlineOMIMSCV000020610.1
      SubmitterFamiliesIndividualsAllele originEthnicityGeographic originCitations and DatabasesDescription
      Total for all submittersnot provided2germline, unknownnot providednot provided
      Department of Genetics, Reproduction and Fetal Medicine.,Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville.not providednot providedgermlinenot providednot providednot providednot provided
      Diasio Lab, Mayo Clinicnot providednot providedunknownnot providednot providednot providednot provided
      Emory Genetics Laboratory,Emory Universitynot provided2germlinenot providednot providednot provided
      OMIMnot providednot providedgermlinenot providednot providednot provided
      PharmGKBnot providednot providedgermlinenot providednot providedPharmGKB Level of Evidence 1A:…Full description
      SubmitterAllele originIndividualsPhenotypes (Affected status)EthnicityGeographic originCitationsDescription

      Last Updated: Aug 22, 2016