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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: 16-2086743-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2086743&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "16",
      "pos": 2086743,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000219476.9",
      "consequences": [
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 38,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4861A>G",
          "hgvs_p": "p.Ile1621Val",
          "transcript": "NM_000548.5",
          "protein_id": "NP_000539.2",
          "transcript_support_level": null,
          "aa_start": 1621,
          "aa_end": null,
          "aa_length": 1807,
          "cds_start": 4861,
          "cds_end": null,
          "cds_length": 5424,
          "cdna_start": 4971,
          "cdna_end": null,
          "cdna_length": 6415,
          "mane_select": "ENST00000219476.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 38,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4861A>G",
          "hgvs_p": "p.Ile1621Val",
          "transcript": "ENST00000219476.9",
          "protein_id": "ENSP00000219476.3",
          "transcript_support_level": 5,
          "aa_start": 1621,
          "aa_end": null,
          "aa_length": 1807,
          "cds_start": 4861,
          "cds_end": null,
          "cds_length": 5424,
          "cdna_start": 4971,
          "cdna_end": null,
          "cdna_length": 6415,
          "mane_select": "NM_000548.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4792A>G",
          "hgvs_p": "p.Ile1598Val",
          "transcript": "ENST00000350773.9",
          "protein_id": "ENSP00000344383.4",
          "transcript_support_level": 1,
          "aa_start": 1598,
          "aa_end": null,
          "aa_length": 1784,
          "cds_start": 4792,
          "cds_end": null,
          "cds_length": 5355,
          "cdna_start": 4867,
          "cdna_end": null,
          "cdna_length": 5538,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 40,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4660A>G",
          "hgvs_p": "p.Ile1554Val",
          "transcript": "ENST00000401874.7",
          "protein_id": "ENSP00000384468.2",
          "transcript_support_level": 1,
          "aa_start": 1554,
          "aa_end": null,
          "aa_length": 1740,
          "cds_start": 4660,
          "cds_end": null,
          "cds_length": 5223,
          "cdna_start": 4766,
          "cdna_end": null,
          "cdna_length": 5437,
          "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": 34,
          "exon_rank_end": null,
          "exon_count": 38,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "n.*4028A>G",
          "hgvs_p": null,
          "transcript": "ENST00000439117.6",
          "protein_id": "ENSP00000406980.2",
          "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": 5073,
          "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": 34,
          "exon_rank_end": null,
          "exon_count": 38,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "n.*4028A>G",
          "hgvs_p": null,
          "transcript": "ENST00000439117.6",
          "protein_id": "ENSP00000406980.2",
          "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": 5073,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 38,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4951A>G",
          "hgvs_p": "p.Ile1651Val",
          "transcript": "ENST00000645186.2",
          "protein_id": "ENSP00000495110.2",
          "transcript_support_level": null,
          "aa_start": 1651,
          "aa_end": null,
          "aa_length": 1837,
          "cds_start": 4951,
          "cds_end": null,
          "cds_length": 5514,
          "cdna_start": 5061,
          "cdna_end": null,
          "cdna_length": 6505,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 38,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4858A>G",
          "hgvs_p": "p.Ile1620Val",
          "transcript": "NM_001406663.1",
          "protein_id": "NP_001393592.1",
          "transcript_support_level": null,
          "aa_start": 1620,
          "aa_end": null,
          "aa_length": 1806,
          "cds_start": 4858,
          "cds_end": null,
          "cds_length": 5421,
          "cdna_start": 4968,
          "cdna_end": null,
          "cdna_length": 6412,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 38,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4858A>G",
          "hgvs_p": "p.Ile1620Val",
          "transcript": "ENST00000642365.2",
          "protein_id": "ENSP00000495459.2",
          "transcript_support_level": null,
          "aa_start": 1620,
          "aa_end": null,
          "aa_length": 1806,
          "cds_start": 4858,
          "cds_end": null,
          "cds_length": 5421,
          "cdna_start": 4929,
          "cdna_end": null,
          "cdna_length": 5574,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 38,
          "exon_rank_end": null,
          "exon_count": 42,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4855A>G",
          "hgvs_p": "p.Ile1619Val",
          "transcript": "ENST00000646388.1",
          "protein_id": "ENSP00000495921.1",
          "transcript_support_level": null,
          "aa_start": 1619,
          "aa_end": null,
          "aa_length": 1805,
          "cds_start": 4855,
          "cds_end": null,
          "cds_length": 5418,
          "cdna_start": 4941,
          "cdna_end": null,
          "cdna_length": 5614,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4792A>G",
          "hgvs_p": "p.Ile1598Val",
          "transcript": "NM_001114382.3",
          "protein_id": "NP_001107854.1",
          "transcript_support_level": null,
          "aa_start": 1598,
          "aa_end": null,
          "aa_length": 1784,
          "cds_start": 4792,
          "cds_end": null,
          "cds_length": 5355,
          "cdna_start": 4902,
          "cdna_end": null,
          "cdna_length": 6346,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4789A>G",
          "hgvs_p": "p.Ile1597Val",
          "transcript": "NM_001406664.1",
          "protein_id": "NP_001393593.1",
          "transcript_support_level": null,
          "aa_start": 1597,
          "aa_end": null,
          "aa_length": 1783,
          "cds_start": 4789,
          "cds_end": null,
          "cds_length": 5352,
          "cdna_start": 4899,
          "cdna_end": null,
          "cdna_length": 6343,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4786A>G",
          "hgvs_p": "p.Ile1596Val",
          "transcript": "ENST00000643946.1",
          "protein_id": "ENSP00000495927.1",
          "transcript_support_level": null,
          "aa_start": 1596,
          "aa_end": null,
          "aa_length": 1782,
          "cds_start": 4786,
          "cds_end": null,
          "cds_length": 5349,
          "cdna_start": 4904,
          "cdna_end": null,
          "cdna_length": 6344,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4783A>G",
          "hgvs_p": "p.Ile1595Val",
          "transcript": "NM_001406665.1",
          "protein_id": "NP_001393594.1",
          "transcript_support_level": null,
          "aa_start": 1595,
          "aa_end": null,
          "aa_length": 1781,
          "cds_start": 4783,
          "cds_end": null,
          "cds_length": 5346,
          "cdna_start": 4893,
          "cdna_end": null,
          "cdna_length": 6337,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 40,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4780A>G",
          "hgvs_p": "p.Ile1594Val",
          "transcript": "ENST00000644399.1",
          "protein_id": "ENSP00000493990.1",
          "transcript_support_level": null,
          "aa_start": 1594,
          "aa_end": null,
          "aa_length": 1780,
          "cds_start": 4780,
          "cds_end": null,
          "cds_length": 5343,
          "cdna_start": 4782,
          "cdna_end": null,
          "cdna_length": 5445,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 40,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4753A>G",
          "hgvs_p": "p.Ile1585Val",
          "transcript": "NM_001406667.1",
          "protein_id": "NP_001393596.1",
          "transcript_support_level": null,
          "aa_start": 1585,
          "aa_end": null,
          "aa_length": 1771,
          "cds_start": 4753,
          "cds_end": null,
          "cds_length": 5316,
          "cdna_start": 4863,
          "cdna_end": null,
          "cdna_length": 6307,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 40,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4750A>G",
          "hgvs_p": "p.Ile1584Val",
          "transcript": "NM_001406668.1",
          "protein_id": "NP_001393597.1",
          "transcript_support_level": null,
          "aa_start": 1584,
          "aa_end": null,
          "aa_length": 1770,
          "cds_start": 4750,
          "cds_end": null,
          "cds_length": 5313,
          "cdna_start": 4860,
          "cdna_end": null,
          "cdna_length": 6304,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4660A>G",
          "hgvs_p": "p.Ile1554Val",
          "transcript": "ENST00000644329.1",
          "protein_id": "ENSP00000496611.1",
          "transcript_support_level": null,
          "aa_start": 1554,
          "aa_end": null,
          "aa_length": 1769,
          "cds_start": 4660,
          "cds_end": null,
          "cds_length": 5310,
          "cdna_start": 4722,
          "cdna_end": null,
          "cdna_length": 5453,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4732A>G",
          "hgvs_p": "p.Ile1578Val",
          "transcript": "NM_021055.3",
          "protein_id": "NP_066399.2",
          "transcript_support_level": null,
          "aa_start": 1578,
          "aa_end": null,
          "aa_length": 1764,
          "cds_start": 4732,
          "cds_end": null,
          "cds_length": 5295,
          "cdna_start": 4842,
          "cdna_end": null,
          "cdna_length": 6286,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TSC2",
          "gene_hgnc_id": 12363,
          "hgvs_c": "c.4732A>G",
          "hgvs_p": "p.Ile1578Val",
          "transcript": "ENST00000644043.1",
          "protein_id": "ENSP00000496262.1",
          "transcript_support_level": null,
          "aa_start": 1578,
          "aa_end": null,
          "aa_length": 1764,
          "cds_start": 4732,
          "cds_end": null,
          "cds_length": 5295,
          "cdna_start": 4786,
          "cdna_end": null,
          "cdna_length": 5457,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 37,
          "exon_rank_end": null,
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        },
        {
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          ],
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          "cdna_length": 6179,
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        }
      ],
      "gene_symbol": "TSC2",
      "gene_hgnc_id": 12363,
      "dbsnp": "rs1555516628",
      "frequency_reference_population": 0.000003428631,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 5,
      "gnomad_exomes_af": 0.00000342863,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 5,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.5765770673751831,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.612,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.1253,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.06,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 7.487,
      "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": 0,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM1,PM2,BS2",
      "acmg_by_gene": [
        {
          "score": 0,
          "benign_score": 4,
          "pathogenic_score": 4,
          "criteria": [
            "PM1",
            "PM2",
            "BS2"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000219476.9",
          "gene_symbol": "TSC2",
          "hgnc_id": 12363,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.4861A>G",
          "hgvs_p": "p.Ile1621Val"
        }
      ],
      "clinvar_disease": "Hereditary cancer-predisposing syndrome,Isolated focal cortical dysplasia type II,Tuberous sclerosis 2,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:4 B:1",
      "phenotype_combined": "Tuberous sclerosis 2|Hereditary cancer-predisposing syndrome|not provided|Isolated focal cortical dysplasia type II",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}