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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: 5-112843860-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=112843860&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "5",
      "pos": 112843860,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000257430.9",
      "consequences": [
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "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.8266A>G",
          "hgvs_p": "p.Ile2756Val",
          "transcript": "NM_000038.6",
          "protein_id": "NP_000029.2",
          "transcript_support_level": null,
          "aa_start": 2756,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 8266,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 8325,
          "cdna_end": null,
          "cdna_length": 10704,
          "mane_select": "ENST00000257430.9",
          "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": 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.8266A>G",
          "hgvs_p": "p.Ile2756Val",
          "transcript": "ENST00000257430.9",
          "protein_id": "ENSP00000257430.4",
          "transcript_support_level": 5,
          "aa_start": 2756,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 8266,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 8325,
          "cdna_end": null,
          "cdna_length": 10704,
          "mane_select": "NM_000038.6",
          "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": 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.8266A>G",
          "hgvs_p": "p.Ile2756Val",
          "transcript": "ENST00000508376.6",
          "protein_id": "ENSP00000427089.2",
          "transcript_support_level": 1,
          "aa_start": 2756,
          "aa_end": null,
          "aa_length": 2843,
          "cds_start": 8266,
          "cds_end": null,
          "cds_length": 8532,
          "cdna_start": 8423,
          "cdna_end": null,
          "cdna_length": 10619,
          "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.229-12789A>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": "I",
          "aa_alt": "V",
          "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.8350A>G",
          "hgvs_p": "p.Ile2784Val",
          "transcript": "NM_001407446.1",
          "protein_id": "NP_001394375.1",
          "transcript_support_level": null,
          "aa_start": 2784,
          "aa_end": null,
          "aa_length": 2871,
          "cds_start": 8350,
          "cds_end": null,
          "cds_length": 8616,
          "cdna_start": 8570,
          "cdna_end": null,
          "cdna_length": 10949,
          "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": 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.8320A>G",
          "hgvs_p": "p.Ile2774Val",
          "transcript": "NM_001354896.2",
          "protein_id": "NP_001341825.1",
          "transcript_support_level": null,
          "aa_start": 2774,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 8320,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 8379,
          "cdna_end": null,
          "cdna_length": 10758,
          "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": 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.8320A>G",
          "hgvs_p": "p.Ile2774Val",
          "transcript": "NM_001407447.1",
          "protein_id": "NP_001394376.1",
          "transcript_support_level": null,
          "aa_start": 2774,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 8320,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 8723,
          "cdna_end": null,
          "cdna_length": 11102,
          "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": 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.8320A>G",
          "hgvs_p": "p.Ile2774Val",
          "transcript": "NM_001407448.1",
          "protein_id": "NP_001394377.1",
          "transcript_support_level": null,
          "aa_start": 2774,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 8320,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 8490,
          "cdna_end": null,
          "cdna_length": 10869,
          "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": 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.8320A>G",
          "hgvs_p": "p.Ile2774Val",
          "transcript": "NM_001407449.1",
          "protein_id": "NP_001394378.1",
          "transcript_support_level": null,
          "aa_start": 2774,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 8320,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 8487,
          "cdna_end": null,
          "cdna_length": 10866,
          "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": 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.8320A>G",
          "hgvs_p": "p.Ile2774Val",
          "transcript": "ENST00000504915.3",
          "protein_id": "ENSP00000473355.2",
          "transcript_support_level": 5,
          "aa_start": 2774,
          "aa_end": null,
          "aa_length": 2861,
          "cds_start": 8320,
          "cds_end": null,
          "cds_length": 8586,
          "cdna_start": 8376,
          "cdna_end": null,
          "cdna_length": 9496,
          "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": 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.8296A>G",
          "hgvs_p": "p.Ile2766Val",
          "transcript": "NM_001354897.2",
          "protein_id": "NP_001341826.1",
          "transcript_support_level": null,
          "aa_start": 2766,
          "aa_end": null,
          "aa_length": 2853,
          "cds_start": 8296,
          "cds_end": null,
          "cds_length": 8562,
          "cdna_start": 8516,
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          "cdna_length": 10895,
          "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": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
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          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.8266A>G",
          "hgvs_p": "p.Ile2756Val",
          "transcript": "NM_001127510.3",
          "protein_id": "NP_001120982.1",
          "transcript_support_level": null,
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          "cds_start": 8266,
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          "mane_select": null,
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        },
        {
          "aa_ref": "I",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 16,
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          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.8266A>G",
          "hgvs_p": "p.Ile2756Val",
          "transcript": "NM_001354895.2",
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          "aa_start": 2756,
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        {
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.8266A>G",
          "hgvs_p": "p.Ile2756Val",
          "transcript": "NM_001407450.1",
          "protein_id": "NP_001394379.1",
          "transcript_support_level": null,
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          "cds_start": 8266,
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        },
        {
          "aa_ref": "I",
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          ],
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          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
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          "hgvs_p": "p.Ile2756Val",
          "transcript": "ENST00000509732.6",
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        },
        {
          "aa_ref": "I",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 16,
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          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.8266A>G",
          "hgvs_p": "p.Ile2756Val",
          "transcript": "ENST00000512211.7",
          "protein_id": "ENSP00000423828.3",
          "transcript_support_level": 2,
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          "cds_start": 8266,
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        },
        {
          "aa_ref": "I",
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          "canonical": false,
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          "consequences": [
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          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
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          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.8245A>G",
          "hgvs_p": "p.Ile2749Val",
          "transcript": "NM_001407451.1",
          "protein_id": "NP_001394380.1",
          "transcript_support_level": null,
          "aa_start": 2749,
          "aa_end": null,
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          "cds_start": 8245,
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          "cdna_start": 8334,
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        },
        {
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          "intron_rank": null,
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          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.8236A>G",
          "hgvs_p": "p.Ile2746Val",
          "transcript": "NM_001407452.1",
          "protein_id": "NP_001394381.1",
          "transcript_support_level": null,
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        },
        {
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          ],
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          "exon_count": 14,
          "intron_rank": null,
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          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.8212A>G",
          "hgvs_p": "p.Ile2738Val",
          "transcript": "NM_001127511.3",
          "protein_id": "NP_001120983.2",
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          "feature": null
        },
        {
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          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "APC",
          "gene_hgnc_id": 583,
          "hgvs_c": "c.8212A>G",
          "hgvs_p": "p.Ile2738Val",
          "transcript": "ENST00000507379.6",
          "protein_id": "ENSP00000423224.2",
          "transcript_support_level": 2,
          "aa_start": 2738,
          "aa_end": null,
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          "cds_start": 8212,
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          "cds_length": 8478,
          "cdna_start": 8408,
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          "cdna_length": 8674,
          "mane_select": null,
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          "biotype": null,
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        },
        {
          "aa_ref": "I",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
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      ],
      "gene_symbol": "APC",
      "gene_hgnc_id": 583,
      "dbsnp": "rs146115809",
      "frequency_reference_population": 0.000053901076,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 87,
      "gnomad_exomes_af": 0.0000321532,
      "gnomad_genomes_af": 0.000262615,
      "gnomad_exomes_ac": 47,
      "gnomad_genomes_ac": 40,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.0198972225189209,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.364,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.0562,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.3,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.294,
      "phylop100way_prediction": "Benign",
      "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": -5,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Strong,BP6",
      "acmg_by_gene": [
        {
          "score": -5,
          "benign_score": 5,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000257430.9",
          "gene_symbol": "APC",
          "hgnc_id": 583,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.8266A>G",
          "hgvs_p": "p.Ile2756Val"
        },
        {
          "score": -5,
          "benign_score": 5,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000520401.1",
          "gene_symbol": "ENSG00000258864",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.229-12789A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " hereditary,APC-Associated Polyposis Disorders,Colorectal adenoma,Desmoid disease,Familial adenomatous polyposis 1,Hereditary cancer-predisposing syndrome,Ovarian cancer,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:4 LB:11 B:1",
      "phenotype_combined": "Familial adenomatous polyposis 1|Colorectal adenoma|not provided|Hereditary cancer-predisposing syndrome|not specified|APC-Associated Polyposis Disorders|Desmoid disease, hereditary;Familial adenomatous polyposis 1|Ovarian cancer",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}