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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: 3-49419292-G-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49419292&ref=G&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 49419292,
      "ref": "G",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000273588.9",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.664C>A",
          "hgvs_p": "p.Arg222Ser",
          "transcript": "NM_000481.4",
          "protein_id": "NP_000472.2",
          "transcript_support_level": null,
          "aa_start": 222,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 664,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 687,
          "cdna_end": null,
          "cdna_length": 1997,
          "mane_select": "ENST00000273588.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.664C>A",
          "hgvs_p": "p.Arg222Ser",
          "transcript": "ENST00000273588.9",
          "protein_id": "ENSP00000273588.3",
          "transcript_support_level": 1,
          "aa_start": 222,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 664,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 687,
          "cdna_end": null,
          "cdna_length": 1997,
          "mane_select": "NM_000481.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000283189",
          "gene_hgnc_id": null,
          "hgvs_c": "c.901C>A",
          "hgvs_p": "p.Arg301Ser",
          "transcript": "ENST00000636166.1",
          "protein_id": "ENSP00000490106.1",
          "transcript_support_level": 5,
          "aa_start": 301,
          "aa_end": null,
          "aa_length": 482,
          "cds_start": 901,
          "cds_end": null,
          "cds_length": 1449,
          "cdna_start": 972,
          "cdna_end": null,
          "cdna_length": 2266,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.664C>A",
          "hgvs_p": "p.Arg222Ser",
          "transcript": "ENST00000395338.7",
          "protein_id": "ENSP00000378747.2",
          "transcript_support_level": 1,
          "aa_start": 222,
          "aa_end": null,
          "aa_length": 386,
          "cds_start": 664,
          "cds_end": null,
          "cds_length": 1161,
          "cdna_start": 768,
          "cdna_end": null,
          "cdna_length": 1831,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.664C>A",
          "hgvs_p": "p.Arg222Ser",
          "transcript": "NM_001164712.2",
          "protein_id": "NP_001158184.1",
          "transcript_support_level": null,
          "aa_start": 222,
          "aa_end": null,
          "aa_length": 386,
          "cds_start": 664,
          "cds_end": null,
          "cds_length": 1161,
          "cdna_start": 687,
          "cdna_end": null,
          "cdna_length": 1750,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.583C>A",
          "hgvs_p": "p.Arg195Ser",
          "transcript": "ENST00000638063.1",
          "protein_id": "ENSP00000489760.1",
          "transcript_support_level": 5,
          "aa_start": 195,
          "aa_end": null,
          "aa_length": 376,
          "cds_start": 583,
          "cds_end": null,
          "cds_length": 1131,
          "cdna_start": 593,
          "cdna_end": null,
          "cdna_length": 1783,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.532C>A",
          "hgvs_p": "p.Arg178Ser",
          "transcript": "NM_001164710.2",
          "protein_id": "NP_001158182.1",
          "transcript_support_level": null,
          "aa_start": 178,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 532,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": 555,
          "cdna_end": null,
          "cdna_length": 1865,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.532C>A",
          "hgvs_p": "p.Arg178Ser",
          "transcript": "ENST00000458307.6",
          "protein_id": "ENSP00000415619.2",
          "transcript_support_level": 2,
          "aa_start": 178,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 532,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": 551,
          "cdna_end": null,
          "cdna_length": 1860,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.583C>A",
          "hgvs_p": "p.Arg195Ser",
          "transcript": "ENST00000635808.1",
          "protein_id": "ENSP00000489620.1",
          "transcript_support_level": 5,
          "aa_start": 195,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 583,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": 606,
          "cdna_end": null,
          "cdna_length": 1610,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.520C>A",
          "hgvs_p": "p.Arg174Ser",
          "transcript": "ENST00000538581.6",
          "protein_id": "ENSP00000443200.2",
          "transcript_support_level": 2,
          "aa_start": 174,
          "aa_end": null,
          "aa_length": 355,
          "cds_start": 520,
          "cds_end": null,
          "cds_length": 1068,
          "cdna_start": 729,
          "cdna_end": null,
          "cdna_length": 2038,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.508C>A",
          "hgvs_p": "p.Arg170Ser",
          "transcript": "ENST00000636865.1",
          "protein_id": "ENSP00000490601.1",
          "transcript_support_level": 5,
          "aa_start": 170,
          "aa_end": null,
          "aa_length": 351,
          "cds_start": 508,
          "cds_end": null,
          "cds_length": 1056,
          "cdna_start": 655,
          "cdna_end": null,
          "cdna_length": 1914,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.664C>A",
          "hgvs_p": "p.Arg222Ser",
          "transcript": "ENST00000637682.1",
          "protein_id": "ENSP00000489856.1",
          "transcript_support_level": 5,
          "aa_start": 222,
          "aa_end": null,
          "aa_length": 351,
          "cds_start": 664,
          "cds_end": null,
          "cds_length": 1056,
          "cdna_start": 671,
          "cdna_end": null,
          "cdna_length": 1823,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.496C>A",
          "hgvs_p": "p.Arg166Ser",
          "transcript": "NM_001164711.2",
          "protein_id": "NP_001158183.1",
          "transcript_support_level": null,
          "aa_start": 166,
          "aa_end": null,
          "aa_length": 347,
          "cds_start": 496,
          "cds_end": null,
          "cds_length": 1044,
          "cdna_start": 519,
          "cdna_end": null,
          "cdna_length": 1829,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.496C>A",
          "hgvs_p": "p.Arg166Ser",
          "transcript": "ENST00000636522.1",
          "protein_id": "ENSP00000489758.1",
          "transcript_support_level": 2,
          "aa_start": 166,
          "aa_end": null,
          "aa_length": 347,
          "cds_start": 496,
          "cds_end": null,
          "cds_length": 1044,
          "cdna_start": 519,
          "cdna_end": null,
          "cdna_length": 1620,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.520C>A",
          "hgvs_p": "p.Arg174Ser",
          "transcript": "ENST00000427987.6",
          "protein_id": "ENSP00000403821.2",
          "transcript_support_level": 5,
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          "aa_length": 338,
          "cds_start": 520,
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          "cds_length": 1017,
          "cdna_start": 658,
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          "cdna_length": 1646,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.475C>A",
          "hgvs_p": "p.Arg159Ser",
          "transcript": "ENST00000637455.1",
          "protein_id": "ENSP00000489628.1",
          "transcript_support_level": 5,
          "aa_start": 159,
          "aa_end": null,
          "aa_length": 321,
          "cds_start": 475,
          "cds_end": null,
          "cds_length": 966,
          "cdna_start": 475,
          "cdna_end": null,
          "cdna_length": 1512,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "n.*36C>A",
          "hgvs_p": null,
          "transcript": "ENST00000399379.7",
          "protein_id": "ENSP00000399943.2",
          "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": 977,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "n.*466C>A",
          "hgvs_p": null,
          "transcript": "ENST00000430521.2",
          "protein_id": "ENSP00000388068.2",
          "transcript_support_level": 5,
          "aa_start": null,
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          "cds_start": -4,
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          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 798,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "n.846C>A",
          "hgvs_p": null,
          "transcript": "ENST00000461210.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 850,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "n.2558C>A",
          "hgvs_p": null,
          "transcript": "ENST00000465925.6",
          "protein_id": null,
          "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": 3976,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "n.3172C>A",
          "hgvs_p": null,
          "transcript": "ENST00000473163.2",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
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      "dbsnp": "rs781466698",
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      "computational_score_selected": 0.9790357947349548,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
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      "splice_prediction_selected": "Benign",
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      "revel_prediction": "Pathogenic",
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      "bayesdelnoaf_score": 0.45,
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      "phylop100way_score": 9.553,
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      "spliceai_max_score": 0.03,
      "spliceai_max_prediction": "Benign",
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      "acmg_score": 12,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Moderate",
      "acmg_by_gene": [
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          "criteria": [
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            "PM2",
            "PM5",
            "PP3_Strong",
            "PP5_Moderate"
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          "verdict": "Pathogenic",
          "transcript": "ENST00000273588.9",
          "gene_symbol": "AMT",
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          "effects": [
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          ],
          "inheritance_mode": "AR,Unknown",
          "hgvs_c": "c.664C>A",
          "hgvs_p": "p.Arg222Ser"
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        {
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            "PP5_Moderate"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000636166.1",
          "gene_symbol": "ENSG00000283189",
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          "effects": [
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          ],
          "inheritance_mode": "",
          "hgvs_c": "c.901C>A",
          "hgvs_p": "p.Arg301Ser"
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      ],
      "clinvar_disease": "Glycine encephalopathy",
      "clinvar_classification": "Likely pathogenic",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LP:1",
      "phenotype_combined": "Glycine encephalopathy",
      "pathogenicity_classification_combined": "Likely pathogenic",
      "custom_annotations": null
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  ],
  "message": null
}