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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 12-88049228-ACT-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=88049228&ref=ACT&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "12",
      "pos": 88049228,
      "ref": "ACT",
      "alt": "A",
      "effect": "frameshift_variant",
      "transcript": "ENST00000552810.6",
      "consequences": [
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 54,
          "exon_rank_end": null,
          "exon_count": 54,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.7394_7395delAG",
          "hgvs_p": "p.Glu2465fs",
          "transcript": "NM_025114.4",
          "protein_id": "NP_079390.3",
          "transcript_support_level": null,
          "aa_start": 2465,
          "aa_end": null,
          "aa_length": 2479,
          "cds_start": 7394,
          "cds_end": null,
          "cds_length": 7440,
          "cdna_start": 7611,
          "cdna_end": null,
          "cdna_length": 7824,
          "mane_select": "ENST00000552810.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 54,
          "exon_rank_end": null,
          "exon_count": 54,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.7394_7395delAG",
          "hgvs_p": "p.Glu2465fs",
          "transcript": "ENST00000552810.6",
          "protein_id": "ENSP00000448012.1",
          "transcript_support_level": 1,
          "aa_start": 2465,
          "aa_end": null,
          "aa_length": 2479,
          "cds_start": 7394,
          "cds_end": null,
          "cds_length": 7440,
          "cdna_start": 7611,
          "cdna_end": null,
          "cdna_length": 7824,
          "mane_select": "NM_025114.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.4361_4362delAG",
          "hgvs_p": "p.Glu1454fs",
          "transcript": "ENST00000547691.8",
          "protein_id": "ENSP00000446905.3",
          "transcript_support_level": 1,
          "aa_start": 1454,
          "aa_end": null,
          "aa_length": 1468,
          "cds_start": 4361,
          "cds_end": null,
          "cds_length": 4407,
          "cdna_start": 4364,
          "cdna_end": null,
          "cdna_length": 4577,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RLIG1",
          "gene_hgnc_id": 25322,
          "hgvs_c": "n.*1552_*1553delCT",
          "hgvs_p": null,
          "transcript": "ENST00000550333.5",
          "protein_id": "ENSP00000448194.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2740,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RLIG1",
          "gene_hgnc_id": 25322,
          "hgvs_c": "c.*809_*810delCT",
          "hgvs_p": null,
          "transcript": "NM_001009894.3",
          "protein_id": "NP_001009894.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 325,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 978,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2829,
          "mane_select": "ENST00000356891.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RLIG1",
          "gene_hgnc_id": 25322,
          "hgvs_c": "c.*809_*810delCT",
          "hgvs_p": null,
          "transcript": "ENST00000356891.4",
          "protein_id": "ENSP00000349358.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 325,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 978,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2829,
          "mane_select": "NM_001009894.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RLIG1",
          "gene_hgnc_id": 25322,
          "hgvs_c": "n.*1552_*1553delCT",
          "hgvs_p": null,
          "transcript": "ENST00000550333.5",
          "protein_id": "ENSP00000448194.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2740,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 56,
          "exon_rank_end": null,
          "exon_count": 56,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8255_8256delAG",
          "hgvs_p": "p.Glu2752fs",
          "transcript": "ENST00000675476.1",
          "protein_id": "ENSP00000502161.1",
          "transcript_support_level": null,
          "aa_start": 2752,
          "aa_end": null,
          "aa_length": 2766,
          "cds_start": 8255,
          "cds_end": null,
          "cds_length": 8301,
          "cdna_start": 8483,
          "cdna_end": null,
          "cdna_length": 8696,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 55,
          "exon_rank_end": null,
          "exon_count": 55,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8162_8163delAG",
          "hgvs_p": "p.Glu2721fs",
          "transcript": "ENST00000675833.1",
          "protein_id": "ENSP00000502559.1",
          "transcript_support_level": null,
          "aa_start": 2721,
          "aa_end": null,
          "aa_length": 2735,
          "cds_start": 8162,
          "cds_end": null,
          "cds_length": 8208,
          "cdna_start": 8390,
          "cdna_end": null,
          "cdna_length": 8603,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 55,
          "exon_rank_end": null,
          "exon_count": 55,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.7403_7404delAG",
          "hgvs_p": "p.Glu2468fs",
          "transcript": "ENST00000309041.12",
          "protein_id": "ENSP00000308021.8",
          "transcript_support_level": 5,
          "aa_start": 2468,
          "aa_end": null,
          "aa_length": 2482,
          "cds_start": 7403,
          "cds_end": null,
          "cds_length": 7449,
          "cdna_start": 7631,
          "cdna_end": null,
          "cdna_length": 7844,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 53,
          "exon_rank_end": null,
          "exon_count": 53,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.7373_7374delAG",
          "hgvs_p": "p.Glu2458fs",
          "transcript": "ENST00000675230.1",
          "protein_id": "ENSP00000502503.1",
          "transcript_support_level": null,
          "aa_start": 2458,
          "aa_end": null,
          "aa_length": 2472,
          "cds_start": 7373,
          "cds_end": null,
          "cds_length": 7419,
          "cdna_start": 7601,
          "cdna_end": null,
          "cdna_length": 7814,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 53,
          "exon_rank_end": null,
          "exon_count": 53,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.7271_7272delAG",
          "hgvs_p": "p.Glu2424fs",
          "transcript": "ENST00000673058.2",
          "protein_id": "ENSP00000500665.2",
          "transcript_support_level": null,
          "aa_start": 2424,
          "aa_end": null,
          "aa_length": 2438,
          "cds_start": 7271,
          "cds_end": null,
          "cds_length": 7317,
          "cdna_start": 7499,
          "cdna_end": null,
          "cdna_length": 7712,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 53,
          "exon_rank_end": null,
          "exon_count": 53,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.7229_7230delAG",
          "hgvs_p": "p.Glu2410fs",
          "transcript": "ENST00000675408.1",
          "protein_id": "ENSP00000502298.1",
          "transcript_support_level": null,
          "aa_start": 2410,
          "aa_end": null,
          "aa_length": 2424,
          "cds_start": 7229,
          "cds_end": null,
          "cds_length": 7275,
          "cdna_start": 7457,
          "cdna_end": null,
          "cdna_length": 7670,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 57,
          "exon_rank_end": null,
          "exon_count": 57,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8264_8265delAG",
          "hgvs_p": "p.Glu2755fs",
          "transcript": "XM_011538756.4",
          "protein_id": "XP_011537058.1",
          "transcript_support_level": null,
          "aa_start": 2755,
          "aa_end": null,
          "aa_length": 2769,
          "cds_start": 8264,
          "cds_end": null,
          "cds_length": 8310,
          "cdna_start": 8481,
          "cdna_end": null,
          "cdna_length": 8694,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 57,
          "exon_rank_end": null,
          "exon_count": 57,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8264_8265delAG",
          "hgvs_p": "p.Glu2755fs",
          "transcript": "XM_011538757.4",
          "protein_id": "XP_011537059.1",
          "transcript_support_level": null,
          "aa_start": 2755,
          "aa_end": null,
          "aa_length": 2769,
          "cds_start": 8264,
          "cds_end": null,
          "cds_length": 8310,
          "cdna_start": 8419,
          "cdna_end": null,
          "cdna_length": 8632,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 57,
          "exon_rank_end": null,
          "exon_count": 57,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8261_8262delAG",
          "hgvs_p": "p.Glu2754fs",
          "transcript": "XM_011538758.4",
          "protein_id": "XP_011537060.1",
          "transcript_support_level": null,
          "aa_start": 2754,
          "aa_end": null,
          "aa_length": 2768,
          "cds_start": 8261,
          "cds_end": null,
          "cds_length": 8307,
          "cdna_start": 8478,
          "cdna_end": null,
          "cdna_length": 8691,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 56,
          "exon_rank_end": null,
          "exon_count": 56,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8255_8256delAG",
          "hgvs_p": "p.Glu2752fs",
          "transcript": "XM_011538759.3",
          "protein_id": "XP_011537061.1",
          "transcript_support_level": null,
          "aa_start": 2752,
          "aa_end": null,
          "aa_length": 2766,
          "cds_start": 8255,
          "cds_end": null,
          "cds_length": 8301,
          "cdna_start": 8472,
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          "cdna_length": 8685,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 56,
          "exon_rank_end": null,
          "exon_count": 56,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8141_8142delAG",
          "hgvs_p": "p.Glu2714fs",
          "transcript": "XM_011538760.3",
          "protein_id": "XP_011537062.1",
          "transcript_support_level": null,
          "aa_start": 2714,
          "aa_end": null,
          "aa_length": 2728,
          "cds_start": 8141,
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          "cdna_start": 8358,
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          "cdna_length": 8571,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 55,
          "exon_rank_end": null,
          "exon_count": 55,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8132_8133delAG",
          "hgvs_p": "p.Glu2711fs",
          "transcript": "XM_017019980.3",
          "protein_id": "XP_016875469.1",
          "transcript_support_level": null,
          "aa_start": 2711,
          "aa_end": null,
          "aa_length": 2725,
          "cds_start": 8132,
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          "cds_length": 8178,
          "cdna_start": 8349,
          "cdna_end": null,
          "cdna_length": 8562,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 56,
          "exon_rank_end": null,
          "exon_count": 56,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CEP290",
          "gene_hgnc_id": 29021,
          "hgvs_c": "c.8099_8100delAG",
          "hgvs_p": "p.Glu2700fs",
          "transcript": "XM_011538761.3",
          "protein_id": "XP_011537063.1",
          "transcript_support_level": null,
          "aa_start": 2700,
          "aa_end": null,
          "aa_length": 2714,
          "cds_start": 8099,
          "cds_end": null,
          "cds_length": 8145,
          "cdna_start": 8316,
          "cdna_end": null,
          "cdna_length": 8529,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "E",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 55,
          "exon_rank_end": null,
          "exon_count": 55,
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        {
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          "consequences": [
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          "exon_count": 5,
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          "protein_id": "ENSP00000447327.1",
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      ],
      "gene_symbol": "CEP290",
      "gene_hgnc_id": 29021,
      "dbsnp": "rs569673313",
      "frequency_reference_population": 0.0003066823,
      "hom_count_reference_population": 5,
      "allele_count_reference_population": 492,
      "gnomad_exomes_af": 0.000322943,
      "gnomad_genomes_af": 0.000151318,
      "gnomad_exomes_ac": 469,
      "gnomad_genomes_ac": 23,
      "gnomad_exomes_homalt": 5,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": null,
      "computational_prediction_selected": null,
      "computational_source_selected": null,
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": null,
      "bayesdelnoaf_prediction": null,
      "phylop100way_score": 2.743,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -3,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PVS1_Moderate,BP6,BS2",
      "acmg_by_gene": [
        {
          "score": -3,
          "benign_score": 5,
          "pathogenic_score": 2,
          "criteria": [
            "PVS1_Moderate",
            "BP6",
            "BS2"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000552810.6",
          "gene_symbol": "CEP290",
          "hgnc_id": 29021,
          "effects": [
            "frameshift_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.7394_7395delAG",
          "hgvs_p": "p.Glu2465fs"
        },
        {
          "score": -5,
          "benign_score": 5,
          "pathogenic_score": 0,
          "criteria": [
            "BP6",
            "BS2"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000356891.4",
          "gene_symbol": "RLIG1",
          "hgnc_id": 25322,
          "effects": [
            "3_prime_UTR_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.*809_*810delCT",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " type 4,Bardet-Biedl syndrome 14,CEP290-related disorder,Joubert syndrome,Joubert syndrome 5,Leber congenital amaurosis 10,Meckel syndrome,Meckel-Gruber syndrome,Nephronophthisis,Retinal dystrophy,Senior-Loken syndrome 6,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:4 LB:2 B:2",
      "phenotype_combined": "not specified|Meckel-Gruber syndrome;Joubert syndrome;Nephronophthisis|Joubert syndrome 5|Bardet-Biedl syndrome 14|not provided|Senior-Loken syndrome 6;Meckel syndrome, type 4;Bardet-Biedl syndrome 14;Joubert syndrome 5;Leber congenital amaurosis 10|Retinal dystrophy|CEP290-related disorder",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}