{
  "id": "AIBD-0077",
  "title": "SpliceAI nominates a deep intronic PKHD1 variant in a neonate who died of ARPKD; RNA validation confirms it and the parents proceed to IVF with PGT-M",
  "summary": "SpliceAI scored a deep intronic PKHD1 variant 0.98; RNA studies confirmed aberrant splicing; parents used the diagnosis for IVF with PGT-M.",
  "date_observed": "2024-01-10",
  "date_basis": "unassessed",
  "date_precision": "unassessed",
  "benefit_status": null,
  "source_collection": null,
  "source_entry": null,
  "account": "A male infant was delivered at an outside hospital at 34+2 weeks and had bilateral kidney enlargement with innumerable tiny cysts consistent with autosomal recessive polycystic kidney disease; he was cared for in the Mount Sinai neonatal intensive care unit, New York, and died at two days of life. Whole-genome sequencing found a known paternal pathogenic missense variant, and SpliceAI scores in the NICUnet Rareservoir identified a maternally inherited deep intronic PKHD1 variant scoring 0.98, which RNA studies on maternal urine-derived renal epithelial cells confirmed creates a novel exon with a premature stop codon; GeneDx classified it likely pathogenic. After genetic counseling the parents proceeded with IVF and preimplantation genetic testing for monogenic disorders within one year of the death.",
  "category": "benefit created",
  "unexpected": false,
  "purpose": "SpliceAI is a deep-learning model built to predict the effect of DNA variants on RNA splicing. Nominating a splice-altering deep intronic variant is exactly its intended use.",
  "system": "SpliceAI",
  "model_version": null,
  "developer": "SpliceAI authors (Jaganathan et al., Cell 2019), as cited in the case report; the developing organization is not named in the source text",
  "deployer": "NICUnet consortium / Icahn School of Medicine at Mount Sinai (Rareservoir variant database)",
  "location": "New York, United States",
  "domain": "Healthcare - neonatology / clinical genomics",
  "segment": "Genome reanalysis in a neonatal research network",
  "benefit_type": "Improved Physical Health",
  "taxonomy_note": "The patient had died, so the diagnosis changed the bereaved parents' reproductive planning rather than the infant's outcome.",
  "registry_ids": {},
  "ratings": [
    {
      "group": "personal",
      "depth": 3,
      "reason": "An identifiable family received a definitive molecular cause of their son's death. They used it for IVF with preimplantation genetic testing to avoid a lethal disease recurring. Life-changing for the family, not life-saving for the patient."
    }
  ],
  "ai_role": {
    "status": "assessed",
    "statement": "SpliceAI's score of 0.98 nominated the maternally inherited deep intronic variant as the second allele. Among 78,575 rare intronic PKHD1 variants in gnomAD only one scored higher. Pathogenicity was then established by RT-PCR and Sanger sequencing of maternal urine-derived cells and GeneDx's likely-pathogenic classification. The AI's contribution was candidate selection. Without it the second allele would have remained unexplained. Authors declare no relevant financial interests."
  },
  "evidence": [
    {
      "kind": "case report",
      "citation": "Richter F, Rutherford KD, Cooke AJ, Meshkati M, Eddy-Abrams V, Greene D, Kosowsky J, Park Y, Aggarwal S, Burke RJ, Chang W, Connors J, Giannone PJ, Hays T, Khattar D, Polak M, Senaldi L, Smith-Raska M, Sridhar S, Steiner L, Swanson JR, Tauber KA, Barbosa M, Guttmann KF, Turro E (2024). A Deep Intronic PKHD1 Variant Identified by SpliceAI in a Deceased Neonate With Autosomal Recessive Polycystic Kidney Disease. American Journal of Kidney Diseases 83(6):829-833 (online 10 January 2024).",
      "title": "A Deep Intronic PKHD1 Variant Identified by SpliceAI in a Deceased Neonate With Autosomal Recessive Polycystic Kidney Disease",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11116050/",
      "date": "2024-01-10",
      "written_by": "deployer",
      "quote": "Using SpliceAI scores in the NICUnet Rareservoir, we identified a maternally inherited intronic variant with a score of 0.98 (chr6:52030169 T>C, Figure 1D)."
    },
    {
      "kind": "case report",
      "citation": "Richter F et al. (2024). Am J Kidney Dis 83(6):829-833 (second quotation).",
      "title": "A Deep Intronic PKHD1 Variant Identified by SpliceAI in a Deceased Neonate With Autosomal Recessive Polycystic Kidney Disease",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11116050/",
      "date": "2024-01-10",
      "written_by": "deployer",
      "quote": "After genetic counseling, the parents proceeded with IVF and preimplantation genetic testing for monogenic disorders (PGT-M)."
    },
    {
      "kind": "case report",
      "citation": "Richter F et al. (2024). Am J Kidney Dis 83(6):829-833 (third quotation, GeneDx classification).",
      "title": "A Deep Intronic PKHD1 Variant Identified by SpliceAI in a Deceased Neonate With Autosomal Recessive Polycystic Kidney Disease",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11116050/",
      "date": "2024-01-10",
      "written_by": "deployer",
      "quote": "produced a diagnostic molecular report listing the missense pathogenic variant and classifying the intronic variant as likely pathogenic"
    }
  ],
  "replication": {
    "produced_by": [
      "Whole-genome sequencing with SpliceAI scoring of rare intronic variants in a disease gene already implicated by one pathogenic allele",
      "Access to parental samples for RNA-level validation"
    ],
    "must_hold": [
      "Functional or RNA confirmation before clinical use of the variant",
      "Genetic counseling and access to IVF with PGT-M"
    ],
    "echoes": []
  },
  "paired_incident": null,
  "headline": "SpliceAI nominates a deep intronic PKHD1 variant in fatal ARPKD",
  "metric": "a maternally inherited deep intronic PKHD1 variant scoring 0.98",
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  "later": {
    "status": "unknown",
    "date": null,
    "note": "The parents' IVF with PGT-M within a year of the death is reported in the case report itself; nothing dated after publication was found,.",
    "quote": null,
    "url": null
  },
  "value": null,
  "developer_country": "United States",
  "deployer_country": "United States",
  "unrated_because": null,
  "brief_notes": null,
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    {
      "date": "2026-10-20",
      "change": "Record drafted from the cited sources.",
      "source": null,
      "editor": "AIBD"
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    {
      "date": "2026-10-21",
      "change": "Benefit type set to Improved Physical Health under Trustible's full taxonomy of 23 types; it was Improved Knowledge Discovery among the six first used.",
      "source": "https://trustible.ai/post/a-framework-for-measuring-the-benefits-of-ai/",
      "editor": "AIBD"
    },
    {
      "date": "2026-10-21",
      "change": "Country of the developer and the deployer added from the organization's own site or a registry.",
      "source": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=30661751&retmode=xml; https://en.wikipedia.org/wiki/Icahn_School_of_Medicine_at_Mount_Sinai",
      "editor": "AIBD"
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    {
      "date": "2026-10-21",
      "change": "Prose pass: a rating reason, purpose, the system's part rewritten in shorter sentences with abbreviations expanded; facts, figures and quotations unchanged.",
      "source": null,
      "editor": "AIBD"
    }
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  "confidence": "claimed",
  "shade": "low",
  "claim_status": "The deployer's account",
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}
