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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: 3-49419321-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49419321&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 49419321,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000273588.9",
      "consequences": [
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.635T>C",
          "hgvs_p": "p.Val212Ala",
          "transcript": "NM_000481.4",
          "protein_id": "NP_000472.2",
          "transcript_support_level": null,
          "aa_start": 212,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 635,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 658,
          "cdna_end": null,
          "cdna_length": 1997,
          "mane_select": "ENST00000273588.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.635T>C",
          "hgvs_p": "p.Val212Ala",
          "transcript": "ENST00000273588.9",
          "protein_id": "ENSP00000273588.3",
          "transcript_support_level": 1,
          "aa_start": 212,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 635,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 658,
          "cdna_end": null,
          "cdna_length": 1997,
          "mane_select": "NM_000481.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.872T>C",
          "hgvs_p": "p.Val291Ala",
          "transcript": "ENST00000636166.1",
          "protein_id": "ENSP00000490106.1",
          "transcript_support_level": 5,
          "aa_start": 291,
          "aa_end": null,
          "aa_length": 482,
          "cds_start": 872,
          "cds_end": null,
          "cds_length": 1449,
          "cdna_start": 943,
          "cdna_end": null,
          "cdna_length": 2266,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.635T>C",
          "hgvs_p": "p.Val212Ala",
          "transcript": "ENST00000395338.7",
          "protein_id": "ENSP00000378747.2",
          "transcript_support_level": 1,
          "aa_start": 212,
          "aa_end": null,
          "aa_length": 386,
          "cds_start": 635,
          "cds_end": null,
          "cds_length": 1161,
          "cdna_start": 739,
          "cdna_end": null,
          "cdna_length": 1831,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.635T>C",
          "hgvs_p": "p.Val212Ala",
          "transcript": "NM_001164712.2",
          "protein_id": "NP_001158184.1",
          "transcript_support_level": null,
          "aa_start": 212,
          "aa_end": null,
          "aa_length": 386,
          "cds_start": 635,
          "cds_end": null,
          "cds_length": 1161,
          "cdna_start": 658,
          "cdna_end": null,
          "cdna_length": 1750,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.554T>C",
          "hgvs_p": "p.Val185Ala",
          "transcript": "ENST00000638063.1",
          "protein_id": "ENSP00000489760.1",
          "transcript_support_level": 5,
          "aa_start": 185,
          "aa_end": null,
          "aa_length": 376,
          "cds_start": 554,
          "cds_end": null,
          "cds_length": 1131,
          "cdna_start": 564,
          "cdna_end": null,
          "cdna_length": 1783,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.503T>C",
          "hgvs_p": "p.Val168Ala",
          "transcript": "NM_001164710.2",
          "protein_id": "NP_001158182.1",
          "transcript_support_level": null,
          "aa_start": 168,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 503,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": 526,
          "cdna_end": null,
          "cdna_length": 1865,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.503T>C",
          "hgvs_p": "p.Val168Ala",
          "transcript": "ENST00000458307.6",
          "protein_id": "ENSP00000415619.2",
          "transcript_support_level": 2,
          "aa_start": 168,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 503,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": 522,
          "cdna_end": null,
          "cdna_length": 1860,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.554T>C",
          "hgvs_p": "p.Val185Ala",
          "transcript": "ENST00000635808.1",
          "protein_id": "ENSP00000489620.1",
          "transcript_support_level": 5,
          "aa_start": 185,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 554,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": 577,
          "cdna_end": null,
          "cdna_length": 1610,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.491T>C",
          "hgvs_p": "p.Val164Ala",
          "transcript": "ENST00000538581.6",
          "protein_id": "ENSP00000443200.2",
          "transcript_support_level": 2,
          "aa_start": 164,
          "aa_end": null,
          "aa_length": 355,
          "cds_start": 491,
          "cds_end": null,
          "cds_length": 1068,
          "cdna_start": 700,
          "cdna_end": null,
          "cdna_length": 2038,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.479T>C",
          "hgvs_p": "p.Val160Ala",
          "transcript": "ENST00000636865.1",
          "protein_id": "ENSP00000490601.1",
          "transcript_support_level": 5,
          "aa_start": 160,
          "aa_end": null,
          "aa_length": 351,
          "cds_start": 479,
          "cds_end": null,
          "cds_length": 1056,
          "cdna_start": 626,
          "cdna_end": null,
          "cdna_length": 1914,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.635T>C",
          "hgvs_p": "p.Val212Ala",
          "transcript": "ENST00000637682.1",
          "protein_id": "ENSP00000489856.1",
          "transcript_support_level": 5,
          "aa_start": 212,
          "aa_end": null,
          "aa_length": 351,
          "cds_start": 635,
          "cds_end": null,
          "cds_length": 1056,
          "cdna_start": 642,
          "cdna_end": null,
          "cdna_length": 1823,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.467T>C",
          "hgvs_p": "p.Val156Ala",
          "transcript": "NM_001164711.2",
          "protein_id": "NP_001158183.1",
          "transcript_support_level": null,
          "aa_start": 156,
          "aa_end": null,
          "aa_length": 347,
          "cds_start": 467,
          "cds_end": null,
          "cds_length": 1044,
          "cdna_start": 490,
          "cdna_end": null,
          "cdna_length": 1829,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.467T>C",
          "hgvs_p": "p.Val156Ala",
          "transcript": "ENST00000636522.1",
          "protein_id": "ENSP00000489758.1",
          "transcript_support_level": 2,
          "aa_start": 156,
          "aa_end": null,
          "aa_length": 347,
          "cds_start": 467,
          "cds_end": null,
          "cds_length": 1044,
          "cdna_start": 490,
          "cdna_end": null,
          "cdna_length": 1620,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.491T>C",
          "hgvs_p": "p.Val164Ala",
          "transcript": "ENST00000427987.6",
          "protein_id": "ENSP00000403821.2",
          "transcript_support_level": 5,
          "aa_start": 164,
          "aa_end": null,
          "aa_length": 338,
          "cds_start": 491,
          "cds_end": null,
          "cds_length": 1017,
          "cdna_start": 629,
          "cdna_end": null,
          "cdna_length": 1646,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "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.446T>C",
          "hgvs_p": "p.Val149Ala",
          "transcript": "ENST00000637455.1",
          "protein_id": "ENSP00000489628.1",
          "transcript_support_level": 5,
          "aa_start": 149,
          "aa_end": null,
          "aa_length": 321,
          "cds_start": 446,
          "cds_end": null,
          "cds_length": 966,
          "cdna_start": 446,
          "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.*7T>C",
          "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.*437T>C",
          "hgvs_p": null,
          "transcript": "ENST00000430521.2",
          "protein_id": "ENSP00000388068.2",
          "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": 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.817T>C",
          "hgvs_p": null,
          "transcript": "ENST00000461210.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": 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.2529T>C",
          "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.3143T>C",
          "hgvs_p": null,
          "transcript": "ENST00000473163.2",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
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      ],
      "gene_symbol": "AMT",
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      "dbsnp": "rs201141125",
      "frequency_reference_population": 0.00035636727,
      "hom_count_reference_population": 1,
      "allele_count_reference_population": 575,
      "gnomad_exomes_af": 0.00036597,
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      "gnomad_exomes_ac": 535,
      "gnomad_genomes_ac": 40,
      "gnomad_exomes_homalt": 1,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.8008438348770142,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.10000000149011612,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.887,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.4489,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.38,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 8.909,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0.1,
      "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": 1,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PP3",
      "acmg_by_gene": [
        {
          "score": 1,
          "benign_score": 0,
          "pathogenic_score": 1,
          "criteria": [
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000273588.9",
          "gene_symbol": "AMT",
          "hgnc_id": 473,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,Unknown",
          "hgvs_c": "c.635T>C",
          "hgvs_p": "p.Val212Ala"
        },
        {
          "score": 1,
          "benign_score": 0,
          "pathogenic_score": 1,
          "criteria": [
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          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000636166.1",
          "gene_symbol": "ENSG00000283189",
          "hgnc_id": null,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.872T>C",
          "hgvs_p": "p.Val291Ala"
        }
      ],
      "clinvar_disease": "Glycine encephalopathy,Glycine encephalopathy 2,Inborn genetic diseases,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "P:1 US:9",
      "phenotype_combined": "Glycine encephalopathy|Glycine encephalopathy 2|not provided|Inborn genetic diseases|not specified",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}