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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: 9-37770723-A-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=37770723&ref=A&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "9",
      "pos": 37770723,
      "ref": "A",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_144964.4",
      "consequences": [
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.704A>T",
          "hgvs_p": "p.Asp235Val",
          "transcript": "NM_144964.4",
          "protein_id": "NP_659401.2",
          "transcript_support_level": null,
          "aa_start": 235,
          "aa_end": null,
          "aa_length": 316,
          "cds_start": 704,
          "cds_end": null,
          "cds_length": 951,
          "cdna_start": 781,
          "cdna_end": null,
          "cdna_length": 2293,
          "mane_select": "ENST00000297994.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.704A>T",
          "hgvs_p": "p.Asp235Val",
          "transcript": "ENST00000297994.4",
          "protein_id": "ENSP00000297994.3",
          "transcript_support_level": 1,
          "aa_start": 235,
          "aa_end": null,
          "aa_length": 316,
          "cds_start": 704,
          "cds_end": null,
          "cds_length": 951,
          "cdna_start": 781,
          "cdna_end": null,
          "cdna_length": 2293,
          "mane_select": "NM_144964.4",
          "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": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "n.*291A>T",
          "hgvs_p": null,
          "transcript": "ENST00000488673.6",
          "protein_id": "ENSP00000437395.1",
          "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": 1443,
          "mane_select": null,
          "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": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "n.*291A>T",
          "hgvs_p": null,
          "transcript": "ENST00000488673.6",
          "protein_id": "ENSP00000437395.1",
          "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": 1443,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": 9,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000255872",
          "gene_hgnc_id": null,
          "hgvs_c": "n.*910+13191T>A",
          "hgvs_p": null,
          "transcript": "ENST00000540557.1",
          "protein_id": "ENSP00000457548.1",
          "transcript_support_level": 5,
          "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": 2591,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.551A>T",
          "hgvs_p": "p.Asp184Val",
          "transcript": "NM_001286950.2",
          "protein_id": "NP_001273879.1",
          "transcript_support_level": null,
          "aa_start": 184,
          "aa_end": null,
          "aa_length": 256,
          "cds_start": 551,
          "cds_end": null,
          "cds_length": 771,
          "cdna_start": 628,
          "cdna_end": null,
          "cdna_length": 2113,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.551A>T",
          "hgvs_p": "p.Asp184Val",
          "transcript": "ENST00000537911.5",
          "protein_id": "ENSP00000444997.1",
          "transcript_support_level": 2,
          "aa_start": 184,
          "aa_end": null,
          "aa_length": 256,
          "cds_start": 551,
          "cds_end": null,
          "cds_length": 771,
          "cdna_start": 630,
          "cdna_end": null,
          "cdna_length": 2108,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.470A>T",
          "hgvs_p": "p.Asp157Val",
          "transcript": "NM_001286952.2",
          "protein_id": "NP_001273881.1",
          "transcript_support_level": null,
          "aa_start": 157,
          "aa_end": null,
          "aa_length": 229,
          "cds_start": 470,
          "cds_end": null,
          "cds_length": 690,
          "cdna_start": 547,
          "cdna_end": null,
          "cdna_length": 2032,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.470A>T",
          "hgvs_p": "p.Asp157Val",
          "transcript": "ENST00000377753.6",
          "protein_id": "ENSP00000366982.2",
          "transcript_support_level": 2,
          "aa_start": 157,
          "aa_end": null,
          "aa_length": 229,
          "cds_start": 470,
          "cds_end": null,
          "cds_length": 690,
          "cdna_start": 549,
          "cdna_end": null,
          "cdna_length": 2027,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.419A>T",
          "hgvs_p": "p.Asp140Val",
          "transcript": "NM_001286951.2",
          "protein_id": "NP_001273880.1",
          "transcript_support_level": null,
          "aa_start": 140,
          "aa_end": null,
          "aa_length": 221,
          "cds_start": 419,
          "cds_end": null,
          "cds_length": 666,
          "cdna_start": 672,
          "cdna_end": null,
          "cdna_length": 2184,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.419A>T",
          "hgvs_p": "p.Asp140Val",
          "transcript": "ENST00000377754.6",
          "protein_id": "ENSP00000366983.2",
          "transcript_support_level": 2,
          "aa_start": 140,
          "aa_end": null,
          "aa_length": 221,
          "cds_start": 419,
          "cds_end": null,
          "cds_length": 666,
          "cdna_start": 660,
          "cdna_end": null,
          "cdna_length": 1881,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.371A>T",
          "hgvs_p": "p.Asp124Val",
          "transcript": "NM_001286953.2",
          "protein_id": "NP_001273882.1",
          "transcript_support_level": null,
          "aa_start": 124,
          "aa_end": null,
          "aa_length": 196,
          "cds_start": 371,
          "cds_end": null,
          "cds_length": 591,
          "cdna_start": 536,
          "cdna_end": null,
          "cdna_length": 2021,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.371A>T",
          "hgvs_p": "p.Asp124Val",
          "transcript": "NM_001286954.2",
          "protein_id": "NP_001273883.1",
          "transcript_support_level": null,
          "aa_start": 124,
          "aa_end": null,
          "aa_length": 196,
          "cds_start": 371,
          "cds_end": null,
          "cds_length": 591,
          "cdna_start": 624,
          "cdna_end": null,
          "cdna_length": 2109,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.743A>T",
          "hgvs_p": "p.Asp248Val",
          "transcript": "XM_011517735.4",
          "protein_id": "XP_011516037.1",
          "transcript_support_level": null,
          "aa_start": 248,
          "aa_end": null,
          "aa_length": 329,
          "cds_start": 743,
          "cds_end": null,
          "cds_length": 990,
          "cdna_start": 1126,
          "cdna_end": null,
          "cdna_length": 2638,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.743A>T",
          "hgvs_p": "p.Asp248Val",
          "transcript": "XM_011517736.4",
          "protein_id": "XP_011516038.1",
          "transcript_support_level": null,
          "aa_start": 248,
          "aa_end": null,
          "aa_length": 320,
          "cds_start": 743,
          "cds_end": null,
          "cds_length": 963,
          "cdna_start": 1126,
          "cdna_end": null,
          "cdna_length": 2611,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.704A>T",
          "hgvs_p": "p.Asp235Val",
          "transcript": "XM_024447426.2",
          "protein_id": "XP_024303194.1",
          "transcript_support_level": null,
          "aa_start": 235,
          "aa_end": null,
          "aa_length": 307,
          "cds_start": 704,
          "cds_end": null,
          "cds_length": 924,
          "cdna_start": 781,
          "cdna_end": null,
          "cdna_length": 2266,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.743A>T",
          "hgvs_p": "p.Asp248Val",
          "transcript": "XM_047422833.1",
          "protein_id": "XP_047278789.1",
          "transcript_support_level": null,
          "aa_start": 248,
          "aa_end": null,
          "aa_length": 295,
          "cds_start": 743,
          "cds_end": null,
          "cds_length": 888,
          "cdna_start": 1126,
          "cdna_end": null,
          "cdna_length": 1546,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.743A>T",
          "hgvs_p": "p.Asp248Val",
          "transcript": "XM_017014313.3",
          "protein_id": "XP_016869802.1",
          "transcript_support_level": null,
          "aa_start": 248,
          "aa_end": null,
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          "cds_start": 743,
          "cds_end": null,
          "cds_length": 858,
          "cdna_start": 1126,
          "cdna_end": null,
          "cdna_length": 6519,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.509A>T",
          "hgvs_p": "p.Asp170Val",
          "transcript": "XM_011517738.3",
          "protein_id": "XP_011516040.1",
          "transcript_support_level": null,
          "aa_start": 170,
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          "aa_length": 251,
          "cds_start": 509,
          "cds_end": null,
          "cds_length": 756,
          "cdna_start": 892,
          "cdna_end": null,
          "cdna_length": 2404,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.509A>T",
          "hgvs_p": "p.Asp170Val",
          "transcript": "XM_011517739.4",
          "protein_id": "XP_011516041.1",
          "transcript_support_level": null,
          "aa_start": 170,
          "aa_end": null,
          "aa_length": 242,
          "cds_start": 509,
          "cds_end": null,
          "cds_length": 729,
          "cdna_start": 892,
          "cdna_end": null,
          "cdna_length": 2377,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TRMT10B",
          "gene_hgnc_id": 26454,
          "hgvs_c": "c.470A>T",
          "hgvs_p": "p.Asp157Val",
          "transcript": "XM_005251375.3",
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        },
        {
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        }
      ],
      "gene_symbol": "TRMT10B",
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      "dbsnp": null,
      "frequency_reference_population": 0.000002052458,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 3,
      "gnomad_exomes_af": 0.00000205246,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 3,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9864513874053955,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.773,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9868,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.23,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 7.783,
      "phylop100way_prediction": "Pathogenic",
      "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": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM2,PP3_Strong",
      "acmg_by_gene": [
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_144964.4",
          "gene_symbol": "TRMT10B",
          "hgnc_id": 26454,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.704A>T",
          "hgvs_p": "p.Asp235Val"
        },
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000540557.1",
          "gene_symbol": "ENSG00000255872",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.*910+13191T>A",
          "hgvs_p": null
        },
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000465229.5",
          "gene_symbol": "EXOSC3",
          "hgnc_id": 17944,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "n.*586-3218T>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}