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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: 5-112842318-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=112842318&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "5",
      "pos": 112842318,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000257430.9",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly",
          "transcript": "NM_000038.6",
          "protein_id": "NP_000029.2",
          "transcript_support_level": null,
          "aa_start": 2242,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 6724,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 6783,
          "cdna_end": null,
          "cdna_length": 10704,
          "mane_select": "ENST00000257430.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly",
          "transcript": "ENST00000257430.9",
          "protein_id": "ENSP00000257430.4",
          "transcript_support_level": 5,
          "aa_start": 2242,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 6724,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 6783,
          "cdna_end": null,
          "cdna_length": 10704,
          "mane_select": "NM_000038.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly",
          "transcript": "ENST00000508376.6",
          "protein_id": "ENSP00000427089.2",
          "transcript_support_level": 1,
          "aa_start": 2242,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 6724,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 6881,
          "cdna_end": null,
          "cdna_length": 10619,
          "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": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "n.*6046A>G",
          "hgvs_p": null,
          "transcript": "ENST00000508624.5",
          "protein_id": "ENSP00000424265.1",
          "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": 7406,
          "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": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "n.*6046A>G",
          "hgvs_p": null,
          "transcript": "ENST00000508624.5",
          "protein_id": "ENSP00000424265.1",
          "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": 7406,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000258864",
          "gene_hgnc_id": null,
          "hgvs_c": "n.228+13346A>G",
          "hgvs_p": null,
          "transcript": "ENST00000520401.1",
          "protein_id": "ENSP00000454861.1",
          "transcript_support_level": 3,
          "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": 694,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6808A>G",
          "hgvs_p": "p.Ser2270Gly",
          "transcript": "NM_001407446.1",
          "protein_id": "NP_001394375.1",
          "transcript_support_level": null,
          "aa_start": 2270,
          "aa_end": null,
          "aa_length": 2871,
          "cds_start": 6808,
          "cds_end": null,
          "cds_length": 8616,
          "cdna_start": 7028,
          "cdna_end": null,
          "cdna_length": 10949,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6778A>G",
          "hgvs_p": "p.Ser2260Gly",
          "transcript": "NM_001354896.2",
          "protein_id": "NP_001341825.1",
          "transcript_support_level": null,
          "aa_start": 2260,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 6778,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 6837,
          "cdna_end": null,
          "cdna_length": 10758,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6778A>G",
          "hgvs_p": "p.Ser2260Gly",
          "transcript": "NM_001407447.1",
          "protein_id": "NP_001394376.1",
          "transcript_support_level": null,
          "aa_start": 2260,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 6778,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 7181,
          "cdna_end": null,
          "cdna_length": 11102,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6778A>G",
          "hgvs_p": "p.Ser2260Gly",
          "transcript": "NM_001407448.1",
          "protein_id": "NP_001394377.1",
          "transcript_support_level": null,
          "aa_start": 2260,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 6778,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 6948,
          "cdna_end": null,
          "cdna_length": 10869,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6778A>G",
          "hgvs_p": "p.Ser2260Gly",
          "transcript": "NM_001407449.1",
          "protein_id": "NP_001394378.1",
          "transcript_support_level": null,
          "aa_start": 2260,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 6778,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 6945,
          "cdna_end": null,
          "cdna_length": 10866,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6778A>G",
          "hgvs_p": "p.Ser2260Gly",
          "transcript": "ENST00000504915.3",
          "protein_id": "ENSP00000473355.2",
          "transcript_support_level": 5,
          "aa_start": 2260,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 6778,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 6834,
          "cdna_end": null,
          "cdna_length": 9496,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6754A>G",
          "hgvs_p": "p.Ser2252Gly",
          "transcript": "NM_001354897.2",
          "protein_id": "NP_001341826.1",
          "transcript_support_level": null,
          "aa_start": 2252,
          "aa_end": null,
          "aa_length": 2853,
          "cds_start": 6754,
          "cds_end": null,
          "cds_length": 8562,
          "cdna_start": 6974,
          "cdna_end": null,
          "cdna_length": 10895,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly",
          "transcript": "NM_001127510.3",
          "protein_id": "NP_001120982.1",
          "transcript_support_level": null,
          "aa_start": 2242,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 6724,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 6891,
          "cdna_end": null,
          "cdna_length": 10812,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly",
          "transcript": "NM_001354895.2",
          "protein_id": "NP_001341824.1",
          "transcript_support_level": null,
          "aa_start": 2242,
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          "aa_length": 2843,
          "cds_start": 6724,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 7127,
          "cdna_end": null,
          "cdna_length": 11048,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly",
          "transcript": "NM_001407450.1",
          "protein_id": "NP_001394379.1",
          "transcript_support_level": null,
          "aa_start": 2242,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 6724,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 6894,
          "cdna_end": null,
          "cdna_length": 10815,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly",
          "transcript": "ENST00000509732.6",
          "protein_id": "ENSP00000426541.2",
          "transcript_support_level": 4,
          "aa_start": 2242,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 6724,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 6874,
          "cdna_end": null,
          "cdna_length": 10616,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly",
          "transcript": "ENST00000512211.7",
          "protein_id": "ENSP00000423828.3",
          "transcript_support_level": 2,
          "aa_start": 2242,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 6724,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 7075,
          "cdna_end": null,
          "cdna_length": 9737,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6703A>G",
          "hgvs_p": "p.Ser2235Gly",
          "transcript": "NM_001407451.1",
          "protein_id": "NP_001394380.1",
          "transcript_support_level": null,
          "aa_start": 2235,
          "aa_end": null,
          "aa_length": 2836,
          "cds_start": 6703,
          "cds_end": null,
          "cds_length": 8511,
          "cdna_start": 6792,
          "cdna_end": null,
          "cdna_length": 10713,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.6694A>G",
          "hgvs_p": "p.Ser2232Gly",
          "transcript": "NM_001407452.1",
          "protein_id": "NP_001394381.1",
          "transcript_support_level": null,
          "aa_start": 2232,
          "aa_end": null,
          "aa_length": 2833,
          "cds_start": 6694,
          "cds_end": null,
          "cds_length": 8502,
          "cdna_start": 7097,
          "cdna_end": null,
          "cdna_length": 11018,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
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        {
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      ],
      "gene_symbol": "APC",
      "gene_hgnc_id": 583,
      "dbsnp": "rs201375478",
      "frequency_reference_population": 0.00009976441,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 161,
      "gnomad_exomes_af": 0.000101257,
      "gnomad_genomes_af": 0.0000854319,
      "gnomad_exomes_ac": 148,
      "gnomad_genomes_ac": 13,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.4038407504558563,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.397,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.373,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.1,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 4.678,
      "phylop100way_prediction": "Uncertain_significance",
      "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": -2,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4,BP6",
      "acmg_by_gene": [
        {
          "score": -2,
          "benign_score": 2,
          "pathogenic_score": 0,
          "criteria": [
            "BP4",
            "BP6"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000257430.9",
          "gene_symbol": "APC",
          "hgnc_id": 583,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.6724A>G",
          "hgvs_p": "p.Ser2242Gly"
        },
        {
          "score": -2,
          "benign_score": 2,
          "pathogenic_score": 0,
          "criteria": [
            "BP4",
            "BP6"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000520401.1",
          "gene_symbol": "ENSG00000258864",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.228+13346A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " hereditary,APC-Associated Polyposis Disorders,APC-related disorder,Carcinoma of colon,Desmoid disease,Familial adenomatous polyposis 1,Familial multiple polyposis syndrome,Hepatocellular carcinoma,Hereditary cancer-predisposing syndrome,Neoplasm of stomach,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:4 LB:9 B:3",
      "phenotype_combined": "not provided|Hereditary cancer-predisposing syndrome|not specified|Familial multiple polyposis syndrome|Familial adenomatous polyposis 1|Carcinoma of colon|Desmoid disease, hereditary;Familial adenomatous polyposis 1;Neoplasm of stomach;Carcinoma of colon;Hepatocellular carcinoma|APC-Associated Polyposis Disorders|APC-related disorder",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}