Available parameters and response documentation is available here

GET /lookup/chr11-117222650-A-?add-ACMG-annotation=1&add-source-databases=bravo%2Cisb_kaviar3&format=api
HTTP 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/json ;utf-8
ETag: "11211943d5cf6653518b0c9fff0f12204c2be167df5455081252bd604d1d69a4"
Vary: Accept

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          "title": "NM_014956.5(CEP164):c.347del (p.Lys116fs) AND Nephronophthisis 15",
          "diseases": [
            {
              "normalized_disease": [
                "Nephronophthisis 15"
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              "names": [
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              "submitter_name": "Labcorp Genetics (formerly Invitae), Labcorp",
              "review_date": 20241030,
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              "origin": "germline",
              "method": "clinical testing",
              "submitter_date": 20250207,
              "diseases": [
                {
                  "symbols": {
                    "medgen": "C3541853"
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              "accession_id": "SCV001727092"
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            {
              "submitter_name": "Fulgent Genetics, Fulgent Genetics",
              "review_date": 20240201,
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              "origin": "germline",
              "method": "clinical testing",
              "submitter_date": 20241220,
              "diseases": [
                {
                  "symbols": {
                    "omim": "614845"
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              "date_updated": 20250125,
              "review_description": "Uncertain significance",
              "clinical_significance": [
                "Uncertain significance"
              ],
              "review_status": "criteria provided, single submitter",
              "accession_id": "SCV005680728"
            },
            {
              "submitter_name": "Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City",
              "review_date": 20201011,
              "submission_description": [],
              "origin": "germline",
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              "submitter_date": 20210113,
              "diseases": [
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                  "symbols": {
                    "omim": "614845"
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                }
              ],
              "date_updated": 20210126,
              "review_description": "Likely pathogenic",
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              "review_status": "no assertion criteria provided",
              "accession_id": "SCV001469288"
            }
          ]
        },
        {
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          ],
          "review_description": "Likely pathogenic",
          "date_created": 20241008,
          "review_date": 20240715,
          "title": "NM_014956.5(CEP164):c.347del (p.Lys116fs) AND CEP164-related disorder",
          "diseases": [
            {
              "names": [
                "Cep164-Related Disorder",
                "Cep164-Related Condition"
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              "submitter_name": "PreventionGenetics, part of Exact Sciences",
              "review_date": 20240715,
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                "The CEP164 c.347delA variant is predicted to result in a frameshift and premature protein termination (p.Lys116Argfs*22). To our knowledge, this variant has not been reported in the literature. This variant is reported in 5.9% of alleles in individuals of Latino descent in gnomAD. Frameshift variants in CEP164 are expected to be pathogenic. This variant is interpreted as likely pathogenic."
              ],
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              ],
              "review_status": "no assertion criteria provided",
              "accession_id": "SCV005347059"
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          "date_created": 20211224,
          "review_date": 20211216,
          "title": "NM_014956.5(CEP164):c.347del (p.Lys116fs) AND not provided",
          "diseases": [
            {
              "symbols": {
                "medgen": "C3661900"
              },
              "names": [
                "Not Provided",
                "None Provided",
                "Reclassified - Adra2C Polymorphism",
                "Reclassified - Adrb1 Polymorphism"
              ]
            }
          ],
          "review_stars": 1,
          "review_status": "criteria provided, single submitter",
          "submission_description": [],
          "variant_id": 10190111172226509001,
          "submissions": [
            {
              "submitter_name": "GeneDx",
              "review_date": 20211216,
              "submission_description": [],
              "origin": "germline",
              "method": "clinical testing",
              "submitter_date": 20211222,
              "diseases": [
                {
                  "names": [
                    "Not Provided"
                  ]
                }
              ],
              "date_updated": 20230304,
              "review_description": "Benign",
              "clinical_significance": [
                "Benign"
              ],
              "review_status": "criteria provided, single submitter",
              "accession_id": "SCV002038650"
            }
          ]
        }
      ],
      "main_data": "conflicting interpretations of pathogenicity **1**",
      "names": [
        "NM_014956.5(CEP164):c.347del (p.Lys116fs)"
      ],
      "variant_type": "Deletion"
    }
  ],
  "publications": {
    "publications": [],
    "genes": [
      {
        "publications": [
          {
            "referenced_by": [
              "GenCC"
            ],
            "pub_med_id": 32367404
          },
          {
            "referenced_by": [
              "GenCC"
            ],
            "pub_med_id": 32055034
          },
          {
            "referenced_by": [
              "GenCC"
            ],
            "pub_med_id": 31248650
          },
          {
            "referenced_by": [
              "PanelApp"
            ],
            "pub_med_id": 30847515
          },
          {
            "referenced_by": [
              "GenCC"
            ],
            "pub_med_id": 28125082
          },
          {
            "referenced_by": [
              "gene2phenotype"
            ],
            "pub_med_id": 27708425
          },
          {
            "referenced_by": [
              "gene2phenotype",
              "GenCC",
              "CGD"
            ],
            "pub_med_id": 22863007
          }
        ],
        "gene_symbol": "CEP164",
        "gene_id": 4000
      }
    ]
  },
  "publication_counts": [
    {
      "type": "variant",
      "id": "10190111172226509001",
      "count": 0
    },
    {
      "type": "gene",
      "id": 4000,
      "count": 45,
      "symbol": "CEP164"
    }
  ],
  "bravo": [
    {
      "version": "Freeze5",
      "filter": "PASS",
      "ac": 1,
      "an": 29118,
      "af": null,
      "het": 1,
      "hom": null,
      "ns": null,
      "vrt": null,
      "main_data": "ƒ = 0.0000343",
      "original_variant": "11-117222647-GA-G"
    }
  ],
  "saphetor_known_pathogenicity": [
    {
      "version": "13-May-2025",
      "items": [
        {
          "annotations": {
            "NCBI ClinVar2": [
              {
                "functions": [
                  "NMD",
                  "coding"
                ],
                "coding_impact": "frameshift",
                "acmg_confirmed": false,
                "acmg_class": "Uncertain Significance",
                "acmg_reannotated": "Benign",
                "source": "NCBI ClinVar2",
                "codon": 116,
                "gene_symbol": "CEP164",
                "hgvs": "K116Rfs*22",
                "transcript": "NM_014956.5",
                "submission_count": 5,
                "review_stars": 1,
                "accession_count": 3,
                "publication_count": 0,
                "clinical_significance": [
                  "conflicting interpretations of pathogenicity"
                ],
                "disease_name": [
                  "Cep164-Related Condition",
                  "Cep164-Related Disorder",
                  "Nephronophthisis 15",
                  "None Provided",
                  "Not Provided"
                ],
                "is_conflicting": true,
                "submissions_b": 2,
                "submissions_p": 2,
                "submissions_vus": 1
              }
            ]
          }
        }
      ]
    }
  ],
  "acmg_annotation": {
    "version_name": "13.5.0",
    "gene_symbol": "CEP164",
    "transcript": "NM_014956.5",
    "transcript_reason": "MANE select",
    "coding_impact": "frameshift",
    "verdict": {
      "ACMG_rules": {
        "benign_score": 9,
        "benign_subscore": "Benign",
        "clinical_score": 1.242,
        "pathogenic_score": 1,
        "pathogenic_subscore": "Uncertain Significance",
        "total_score": -8,
        "verdict": "Benign"
      },
      "classifications": [
        "BA1",
        "BP6",
        "PVS1_Supporting"
      ]
    },
    "classifications": [
      {
        "name": "BA1",
        "met_criteria": true,
        "user_explain": [
          "GnomAD exomes allele frequency = 0.0639 is greater than 0.05 threshold, good gnomAD exomes coverage = 54.3."
        ]
      },
      {
        "name": "BP6",
        "met_criteria": true,
        "user_explain": [
          "Supporting: ClinVar classifies this variant as Uncertain Significance but a high confidence submitter has classified as Benign, 1 star (reviewed Feb '25, 5 submissions of which 1 is from high confidence submitter), associated with Nephronophthisis 15."
        ]
      },
      {
        "name": "PVS1",
        "met_criteria": true,
        "user_explain": [
          "Reduced strength as variant has BA1 frequency. null variant (frame-shift) in gene CEP164, predicted to cause NMD. Loss-of-function is a known mechanism of disease (gene has 122 reported pathogenic LOF variants). The exon affects 4 functional domains: UniProt protein A0A1W2PQ68 region of interest 'Disordered', UniProt protein E9PR73 region of interest 'Disordered', UniProt protein Q9UPV0 region of interest 'Disordered', and UniProt protein Q9UPV0 region of interest 'Interaction with ATRIP'. The exon contains 10 pathogenic variants. The truncated region contains 112 pathogenic variants."
        ],
        "strength": "Supporting"
      }
    ],
    "gene_id": 4000,
    "sample_findings": {
      "phenotypes": "No matching phenotype found for gene CEP164 which is associated with Ciliopathies, Ciliopathy, Ciliopathy Genes Associated With Cystic Kidney Disease, Genetic Retinal Degeneration Conditions, and 7 more, according to CGD, ClinGen Disease Validity, GenCC, Mondo, PanelApp, and gene2phenotype.",
      "mode_of_inheritance": "AR, based on gene information from CGD, ClinGen Disease Validity, GenCC, Mondo, PanelApp, and gene2phenotype."
    }
  },
  "phylop100way": [
    {
      "version": "13-Apr-2021",
      "conservation_score": [
        "5.763",
        "2.286",
        "0.918",
        "4.849",
        "6.917",
        "3.684",
        "6.943",
        "8.715",
        "1.062",
        "5.822",
        "8.715"
      ]
    }
  ],
  "maxentscan": null
}