Available parameters and response documentation is available here

GET /lookup/chr11-117222650-A-?add-ACMG-annotation=1&add-source-databases=bravo,isb_kaviar3
HTTP 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/json ;utf-8
ETag: "7314f08e8e08795c69a62d772c8699f0247c720ec6383fa24b62dfcb5c10638d"
Vary: Accept

{
  "chromosome": "chr11",
  "alt": "",
  "ref": "A",
  "pos": 117222650,
  "variant_id": "10190111172226509001",
  "regions": {
    "uniprot_regions": {
      "version": "08-Dec-2023",
      "items": [
        {
          "absolute_positon": 501983937,
          "amino_acid": "M1-E28,E28-C65,C65-L131,A132-L184,P185-Q229,S230-E255,E256-Q384,E385-L411,D412-Q439,A440-R470,R470-R526,R526-V575,V575-S645,S645-R689,R689-E761,A762-E787,V788-E831,L832-E872,E873-Q920,E921-Q948,E949-E971,E972-S1030,S1030-T1072,N1073-S1093,S1093-K1167...",
          "chromo": "chr11",
          "colour": "255,0,0",
          "description": null,
          "length": 85413,
          "position": 117198570,
          "protein": "CE164_HUMAN",
          "type": "homo_sapiens proteome sequences",
          "pub_med_references": null
        },
        {
          "absolute_positon": 501994670,
          "amino_acid": "M1-Y194",
          "chromo": "chr11",
          "colour": "255,102,0",
          "description": "Interaction with ATRIP",
          "length": 23847,
          "position": 117209303,
          "protein": "CE164_HUMAN",
          "type": "region of interest",
          "pub_med_references": null
        },
        {
          "absolute_positon": 502007997,
          "amino_acid": "G107-S135",
          "chromo": "chr11",
          "colour": "255,102,0",
          "description": "Disordered",
          "length": 9933,
          "position": 117222630,
          "protein": "CE164_HUMAN",
          "type": "region of interest",
          "pub_med_references": null
        }
      ]
    }
  },
  "variant_type": "Deletion (homopolymer)",
  "cytobands": "11q23.3",
  "refseq_transcripts": [
    {
      "items": [
        {
          "name": "NM_014956.5",
          "strand": "+",
          "coding_impact": "frameshift",
          "function": [
            "NMD",
            "coding"
          ],
          "hgvs": "c.347del",
          "hgvs_p1": "K116Rfs*22",
          "hgvs_p3": "p.(Lys116ArgfsTer22)",
          "location": "exon 5 of 33 position 153 of 199",
          "coding_location": "116 of 1461",
          "canonical": true,
          "gene_symbol": "CEP164",
          "splice_distance": "-47",
          "ensembl_support_level": null,
          "ensembl_appris": null,
          "mane_select": "ENST00000278935.8",
          "mane_plus": null,
          "uniprot_id": null
        },
        {
          "name": "NM_001271933.2",
          "strand": "+",
          "coding_impact": "frameshift",
          "function": [
            "NMD",
            "coding"
          ],
          "hgvs": "c.347del",
          "hgvs_p1": "K116Rfs*22",
          "hgvs_p3": "p.(Lys116ArgfsTer22)",
          "location": "exon 4 of 32 position 153 of 199",
          "coding_location": "116 of 1456",
          "canonical": false,
          "gene_symbol": "CEP164",
          "splice_distance": "-47",
          "ensembl_support_level": null,
          "ensembl_appris": null,
          "mane_select": null,
          "mane_plus": null,
          "uniprot_id": null
        }
      ],
      "version": "221"
    }
  ],
  "ensembl_transcripts": [
    {
      "items": [
        {
          "name": "ENST00000278935.3",
          "strand": "+",
          "coding_impact": "frameshift",
          "function": [
            "NMD",
            "coding"
          ],
          "hgvs": "c.347del",
          "hgvs_p1": "K116Rfs*22",
          "hgvs_p3": "p.(Lys116ArgfsTer22)",
          "location": "exon 5 of 33 position 153 of 199",
          "coding_location": "116 of 1461",
          "canonical": true,
          "gene_symbol": "CEP164",
          "splice_distance": "-47",
          "ensembl_support_level": "1",
          "ensembl_appris": "principal1",
          "mane_select": "NM_014956.5",
          "mane_plus": null,
          "uniprot_id": "Q9UPV0"
        },
        {
          "name": "ENST00000525416.1",
          "strand": "+",
          "coding_impact": "frameshift",
          "function": [
            "coding"
          ],
          "hgvs": "c.209del",
          "hgvs_p1": "K70Rfs*22",
          "hgvs_p3": "p.(Lys70ArgfsTer22)",
          "location": "exon 4 of 5 position 153 of 199",
          "coding_location": "70 of 122",
          "canonical": false,
          "gene_symbol": "CEP164",
          "splice_distance": "-47",
          "ensembl_support_level": "3",
          "ensembl_appris": null,
          "mane_select": null,
          "mane_plus": null,
          "uniprot_id": null
        },
        {
          "name": "ENST00000525734.1",
          "strand": "+",
          "coding_impact": null,
          "function": [
            "3'utr"
          ],
          "hgvs": "c.*2del",
          "hgvs_p1": "p.?",
          "hgvs_p3": "p.?",
          "location": "exon 5 of 5 (3'UTR) position 153 of 153",
          "coding_location": null,
          "canonical": false,
          "gene_symbol": "CEP164",
          "splice_distance": "153",
          "ensembl_support_level": "2",
          "ensembl_appris": null,
          "mane_select": null,
          "mane_plus": null,
          "uniprot_id": null
        },
        {
          "name": "ENST00000527609.1",
          "strand": "+",
          "coding_impact": "frameshift",
          "function": [
            "coding"
          ],
          "hgvs": "c.347del",
          "hgvs_p1": "K116Rfs",
          "hgvs_p3": "p.(Lys116Argfs)",
          "location": "exon 5 of 5 position 153 of 170",
          "coding_location": "116 of 121",
          "canonical": false,
          "gene_symbol": "CEP164",
          "splice_distance": "153",
          "ensembl_support_level": "1",
          "ensembl_appris": null,
          "mane_select": null,
          "mane_plus": null,
          "uniprot_id": null
        },
        {
          "name": "ENST00000533153.1",
          "strand": "+",
          "coding_impact": "frameshift",
          "function": [
            "NMD",
            "coding"
          ],
          "hgvs": "c.209del",
          "hgvs_p1": "K70Rfs*22",
          "hgvs_p3": "p.(Lys70ArgfsTer22)",
          "location": "exon 3 of 5 position 153 of 199",
          "coding_location": "70 of 158",
          "canonical": false,
          "gene_symbol": "CEP164",
          "splice_distance": "-47",
          "ensembl_support_level": "3",
          "ensembl_appris": null,
          "mane_select": null,
          "mane_plus": null,
          "uniprot_id": null
        },
        {
          "name": "ENST00000533570.1",
          "strand": "+",
          "coding_impact": "frameshift",
          "function": [
            "coding"
          ],
          "hgvs": "c.347del",
          "hgvs_p1": "K116Rfs",
          "hgvs_p3": "p.(Lys116Argfs)",
          "location": "exon 4 of 4 position 153 of 171",
          "coding_location": "116 of 121",
          "canonical": false,
          "gene_symbol": "CEP164",
          "splice_distance": "153",
          "ensembl_support_level": "1",
          "ensembl_appris": null,
          "mane_select": null,
          "mane_plus": null,
          "uniprot_id": null
        }
      ],
      "version": "110"
    }
  ],
  "gnomad_exomes": [
    {
      "version": "2.1.1",
      "filter": "PASS",
      "ac": 5026,
      "an": 78708,
      "af": 0.06385627890430452,
      "ac_afr": 311,
      "ac_amr": 637,
      "ac_asj": 145,
      "ac_eas": 303,
      "ac_eas_kor": 50,
      "ac_eas_jpn": 2,
      "ac_eas_oea": 251,
      "ac_fin": 472,
      "ac_nfe": 2514,
      "ac_nfe_bgr": 55,
      "ac_nfe_est": 8,
      "ac_nfe_nwe": 621,
      "ac_nfe_onf": 718,
      "ac_nfe_seu": 405,
      "ac_nfe_swe": 707,
      "ac_oth": 122,
      "ac_sas": 522,
      "ac_afr_male": 126,
      "ac_amr_male": 236,
      "ac_asj_male": 78,
      "ac_eas_male": 159,
      "ac_fin_male": 247,
      "ac_nfe_male": 1479,
      "ac_oth_male": 61,
      "ac_sas_male": 413,
      "ac_afr_female": 185,
      "ac_amr_female": 401,
      "ac_asj_female": 67,
      "ac_eas_female": 144,
      "ac_fin_female": 225,
      "ac_nfe_female": 1035,
      "ac_oth_female": 61,
      "ac_sas_female": 109,
      "ac_male": 2799,
      "ac_female": 2227,
      "an_afr": 5350,
      "an_amr": 10222,
      "an_asj": 3288,
      "an_eas": 5416,
      "an_eas_kor": 1120,
      "an_eas_jpn": 78,
      "an_eas_oea": 4218,
      "an_fin": 7278,
      "an_nfe": 36394,
      "an_nfe_bgr": 966,
      "an_nfe_est": 92,
      "an_nfe_nwe": 13648,
      "an_nfe_onf": 10148,
      "an_nfe_seu": 3530,
      "an_nfe_swe": 8010,
      "an_oth": 1910,
      "an_sas": 8850,
      "an_afr_male": 1976,
      "an_amr_male": 4330,
      "an_asj_male": 1780,
      "an_eas_male": 2692,
      "an_fin_male": 3844,
      "an_nfe_male": 20242,
      "an_oth_male": 988,
      "an_sas_male": 6606,
      "an_afr_female": 3374,
      "an_amr_female": 5892,
      "an_asj_female": 1508,
      "an_eas_female": 2724,
      "an_fin_female": 3434,
      "an_nfe_female": 16152,
      "an_oth_female": 922,
      "an_sas_female": 2244,
      "an_male": 42458,
      "an_female": 36250,
      "age_hist_het_under_30": 119,
      "age_hist_het_30_35": 140,
      "age_hist_het_35_40": 213,
      "age_hist_het_40_45": 443,
      "age_hist_het_45_50": 462,
      "age_hist_het_50_55": 522,
      "age_hist_het_55_60": 532,
      "age_hist_het_60_65": 450,
      "age_hist_het_65_70": 427,
      "age_hist_het_70_75": 309,
      "age_hist_het_75_80": 247,
      "age_hist_het_over_80": 101,
      "variant_type": "mixed",
      "lcr": true,
      "original_variant": "11-117222647-GA-G",
      "main_data": "ƒ = 0.0639"
    }
  ],
  "gnomad_exomes_coverage": [
    {
      "version": "2.1",
      "coverage_mean": [
        54.263999938964844
      ],
      "coverage_median": [
        42.0
      ],
      "coverage_20_frequency": [
        0.9350260933256019
      ]
    }
  ],
  "gnomad_genomes": [
    {
      "version": "2.1.1",
      "filter": "PASS",
      "ac": 30,
      "an": 23226,
      "af": 0.0012916559028674762,
      "ac_afr": 4,
      "ac_amr": 1,
      "ac_eas": 1,
      "ac_fin": 11,
      "ac_nfe": 12,
      "ac_nfe_est": 1,
      "ac_nfe_nwe": 8,
      "ac_nfe_onf": 2,
      "ac_nfe_seu": 1,
      "ac_oth": 1,
      "ac_afr_male": 3,
      "ac_amr_male": 1,
      "ac_eas_male": 1,
      "ac_fin_male": 6,
      "ac_nfe_male": 5,
      "ac_oth_male": 1,
      "ac_afr_female": 1,
      "ac_fin_female": 5,
      "ac_nfe_female": 7,
      "ac_male": 17,
      "ac_female": 13,
      "an_afr": 7398,
      "an_amr": 544,
      "an_asj": 228,
      "an_eas": 1456,
      "an_fin": 1178,
      "an_nfe": 11746,
      "an_nfe_est": 2812,
      "an_nfe_nwe": 7266,
      "an_nfe_onf": 1618,
      "an_nfe_seu": 50,
      "an_oth": 676,
      "an_afr_male": 4276,
      "an_amr_male": 260,
      "an_asj_male": 172,
      "an_eas_male": 968,
      "an_fin_male": 550,
      "an_nfe_male": 6562,
      "an_oth_male": 342,
      "an_afr_female": 3122,
      "an_amr_female": 284,
      "an_asj_female": 56,
      "an_eas_female": 488,
      "an_fin_female": 628,
      "an_nfe_female": 5184,
      "an_oth_female": 334,
      "an_male": 13130,
      "an_female": 10096,
      "age_hist_het_under_30": 3,
      "age_hist_het_30_35": 3,
      "age_hist_het_35_40": 1,
      "age_hist_het_40_45": 2,
      "age_hist_het_45_50": 1,
      "age_hist_het_50_55": 1,
      "age_hist_het_55_60": 2,
      "age_hist_het_65_70": 1,
      "variant_type": "mixed",
      "lcr": true,
      "original_variant": "11-117222647-GA-G",
      "main_data": "ƒ = 0.00129"
    }
  ],
  "gnomad_genomes_coverage": [
    {
      "version": "2.1",
      "coverage_mean": [
        24.854999542236328
      ],
      "coverage_median": [
        25.0
      ],
      "coverage_20_frequency": [
        0.7111423078096866
      ]
    }
  ],
  "isb_kaviar3": [
    {
      "version": "4-Feb-2016",
      "ac": [
        4,
        5,
        12734
      ],
      "an": [
        155504,
        155504,
        155504
      ],
      "main_data": null
    }
  ],
  "ncbi_clinvar2": [
    {
      "version": "07-Feb-2024",
      "review_status": "criteria provided, multiple submitters, no conflicts",
      "review_stars": 2,
      "variation_id": 993033,
      "num_submitters": 3,
      "pub_med_references": null,
      "clinical_significance": [
        "Benign"
      ],
      "last_evaluation": "20230305",
      "origin": null,
      "accessions": [
        {
          "variation_id": 993033,
          "accession_id": "RCV001283852",
          "allele_id": 980941,
          "clinical_significance": [
            "Benign"
          ],
          "submission_description": [],
          "review_date": 20221007,
          "review_description": "Benign",
          "review_status": "criteria provided, single submitter",
          "review_stars": 1,
          "submissions": [
            {
              "submitter_name": "Invitae",
              "submission_description": [],
              "submitter_date": 20230111,
              "review_description": "Benign",
              "review_date": 20221007,
              "origin": "germline",
              "review_status": "criteria provided, single submitter",
              "method": "clinical testing",
              "date_updated": 20230207,
              "diseases": [
                {
                  "symbols": {
                    "medgen": "C3541853"
                  }
                }
              ],
              "clinical_significance": [
                "Benign"
              ],
              "accession_id": "SCV001727092"
            },
            {
              "submitter_name": "Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City",
              "submission_description": [],
              "submitter_date": 20210113,
              "review_description": "Likely pathogenic",
              "review_date": 20201011,
              "origin": "germline",
              "review_status": "no assertion criteria provided",
              "method": "clinical testing",
              "date_updated": 20210126,
              "diseases": [
                {
                  "symbols": {
                    "omim": "614845"
                  }
                }
              ],
              "clinical_significance": [
                "Likely pathogenic"
              ],
              "accession_id": "SCV001469288"
            }
          ],
          "title": "NM_014956.5(CEP164):c.347del (p.Lys116fs) AND Nephronophthisis 15",
          "diseases": [
            {
              "normalized_disease": [
                "Nephronophthisis 15"
              ],
              "symbols": {
                "orphanet": "3156",
                "omim": "614845",
                "medgen": "C3541853",
                "mondo": "MONDO:0013917"
              },
              "names": [
                "Nephronophthisis 15"
              ]
            }
          ],
          "date_created": 20210126,
          "variant_id": 10190111172226509001
        },
        {
          "variation_id": 993033,
          "accession_id": "RCV001797168",
          "allele_id": 980941,
          "clinical_significance": [
            "Benign"
          ],
          "submission_description": [],
          "review_date": 20211216,
          "review_description": "Benign",
          "review_status": "criteria provided, single submitter",
          "review_stars": 1,
          "submissions": [
            {
              "submitter_name": "GeneDx",
              "submission_description": [],
              "submitter_date": 20211222,
              "review_description": "Benign",
              "review_date": 20211216,
              "origin": "germline",
              "review_status": "criteria provided, single submitter",
              "method": "clinical testing",
              "date_updated": 20230304,
              "diseases": [
                {
                  "names": [
                    "Not Provided"
                  ]
                }
              ],
              "clinical_significance": [
                "Benign"
              ],
              "accession_id": "SCV002038650"
            }
          ],
          "title": "NM_014956.5(CEP164):c.347del (p.Lys116fs) AND not provided",
          "diseases": [
            {
              "symbols": {
                "medgen": "CN517202"
              },
              "names": [
                "Not Provided",
                "None Provided"
              ]
            }
          ],
          "date_created": 20211224,
          "variant_id": 10190111172226509001
        }
      ],
      "main_data": "benign **2**",
      "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",
              "GenCC"
            ],
            "pub_med_id": 27708425
          },
          {
            "referenced_by": [
              "dbNSFP"
            ],
            "pub_med_id": 23348840
          },
          {
            "referenced_by": [
              "gene2phenotype",
              "GenCC",
              "CGD",
              "dbNSFP"
            ],
            "pub_med_id": 22863007
          },
          {
            "referenced_by": [
              "dbNSFP"
            ],
            "pub_med_id": 18283122
          },
          {
            "referenced_by": [
              "dbNSFP"
            ],
            "pub_med_id": 17954613
          }
        ],
        "gene_symbol": "CEP164",
        "gene_id": 4000
      }
    ]
  },
  "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": "29-Feb-2024",
      "items": [
        {
          "annotations": {
            "NCBI ClinVar2": [
              {
                "functions": [
                  "NMD",
                  "coding"
                ],
                "coding_impact": "frameshift",
                "acmg_confirmed": true,
                "acmg_class": "Benign",
                "acmg_reannotated": "Benign",
                "source": "NCBI ClinVar2",
                "codon": 116,
                "gene_symbol": "CEP164",
                "hgvs": "K116Rfs*22",
                "transcript": "NM_014956.5",
                "submission_count": 3,
                "review_stars": 2,
                "accession_count": 2,
                "publication_count": 0,
                "clinical_significance": [
                  "benign"
                ],
                "disease_name": [
                  "Nephronophthisis 15",
                  "None Provided",
                  "Not Provided"
                ]
              }
            ]
          }
        }
      ]
    }
  ],
  "acmg_annotation": {
    "version_name": "11.12.0",
    "gene_symbol": "CEP164",
    "transcript": "NM_014956.5",
    "transcript_reason": "MANE select",
    "coding_impact": "frameshift",
    "verdict": {
      "ACMG_rules": {
        "benign_score": 16,
        "benign_subscore": "Benign",
        "clinical_score": 1.2349999999999999,
        "pathogenic_score": 1,
        "pathogenic_subscore": "Uncertain Significance",
        "total_score": -15,
        "verdict": "Benign"
      },
      "classifications": [
        "BA1",
        "BP6_Very Strong",
        "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": [
          "ClinVar classifies this variant as Benign, 2 stars (multiple consistent, reviewed Mar '23, 3 submissions)."
        ],
        "strength": "Very Strong"
      },
      {
        "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 76 reported pathogenic LOF variants). The exon affects 2 functional domains: UniProt protein CE164_HUMAN region of interest 'Disordered' and UniProt protein CE164_HUMAN region of interest 'Interaction with ATRIP'. The exon contains 8 pathogenic variants. The truncated region contains 69 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
}