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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: 6-56642764-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=56642764&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "6",
      "pos": 56642764,
      "ref": "G",
      "alt": "A",
      "effect": "intron_variant",
      "transcript": "ENST00000680361.1",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.25C>T",
          "hgvs_p": "p.Arg9Cys",
          "transcript": "NM_001723.7",
          "protein_id": "NP_001714.1",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 2649,
          "cds_start": 25,
          "cds_end": null,
          "cds_length": 7950,
          "cdna_start": 126,
          "cdna_end": null,
          "cdna_length": 8971,
          "mane_select": null,
          "mane_plus": "ENST00000370765.11",
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.25C>T",
          "hgvs_p": "p.Arg9Cys",
          "transcript": "ENST00000370765.11",
          "protein_id": "ENSP00000359801.6",
          "transcript_support_level": 1,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 2649,
          "cds_start": 25,
          "cds_end": null,
          "cds_length": 7950,
          "cdna_start": 126,
          "cdna_end": null,
          "cdna_length": 8971,
          "mane_select": null,
          "mane_plus": "NM_001723.7",
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 84,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.25C>T",
          "hgvs_p": "p.Arg9Cys",
          "transcript": "ENST00000244364.10",
          "protein_id": "ENSP00000244364.6",
          "transcript_support_level": 1,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 5171,
          "cds_start": 25,
          "cds_end": null,
          "cds_length": 15516,
          "cdna_start": 233,
          "cdna_end": null,
          "cdna_length": 16742,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.25C>T",
          "hgvs_p": "p.Arg9Cys",
          "transcript": "ENST00000439203.5",
          "protein_id": "ENSP00000404924.1",
          "transcript_support_level": 1,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 3059,
          "cds_start": 25,
          "cds_end": null,
          "cds_length": 9180,
          "cdna_start": 25,
          "cdna_end": null,
          "cdna_length": 9180,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.25C>T",
          "hgvs_p": "p.Arg9Cys",
          "transcript": "ENST00000518935.5",
          "protein_id": "ENSP00000431003.1",
          "transcript_support_level": 1,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 1143,
          "cds_start": 25,
          "cds_end": null,
          "cds_length": 3432,
          "cdna_start": 97,
          "cdna_end": null,
          "cdna_length": 3547,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": 15,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1779-261C>T",
          "hgvs_p": null,
          "transcript": "NM_001374736.1",
          "protein_id": "NP_001361665.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 7818,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 23457,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 24709,
          "mane_select": "ENST00000680361.1",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": 15,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1779-261C>T",
          "hgvs_p": null,
          "transcript": "ENST00000680361.1",
          "protein_id": "ENSP00000505098.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 7818,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 23457,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 24709,
          "mane_select": "NM_001374736.1",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 84,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.25C>T",
          "hgvs_p": "p.Arg9Cys",
          "transcript": "NM_015548.5",
          "protein_id": "NP_056363.2",
          "transcript_support_level": null,
          "aa_start": 9,
          "aa_end": null,
          "aa_length": 5171,
          "cds_start": 25,
          "cds_end": null,
          "cds_length": 15516,
          "cdna_start": 126,
          "cdna_end": null,
          "cdna_length": 16626,
          "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": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "n.126C>T",
          "hgvs_p": null,
          "transcript": "ENST00000518828.1",
          "protein_id": null,
          "transcript_support_level": 4,
          "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": 585,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 103,
          "intron_rank": 15,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1806-261C>T",
          "hgvs_p": null,
          "transcript": "NM_001374734.1",
          "protein_id": "NP_001361663.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 7803,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 23412,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 24664,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
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          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 103,
          "intron_rank": 15,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1779-261C>T",
          "hgvs_p": null,
          "transcript": "NM_001374722.1",
          "protein_id": "NP_001361651.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 7794,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 23385,
          "cdna_start": null,
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          "cdna_length": 24637,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 98,
          "intron_rank": 11,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1146-261C>T",
          "hgvs_p": null,
          "transcript": "NM_001374729.1",
          "protein_id": "NP_001361658.1",
          "transcript_support_level": null,
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          "cds_start": -4,
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          "mane_select": null,
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        {
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          "canonical": false,
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          "exon_count": 98,
          "intron_rank": 11,
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          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1146-261C>T",
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          "transcript": "ENST00000361203.7",
          "protein_id": "ENSP00000354508.3",
          "transcript_support_level": 5,
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          "cdna_start": null,
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        {
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          ],
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          "exon_count": 97,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1680-261C>T",
          "hgvs_p": null,
          "transcript": "NM_001144769.5",
          "protein_id": "NP_001138241.1",
          "transcript_support_level": null,
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          "cdna_start": null,
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          "mane_select": null,
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        {
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          ],
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          "gene_symbol": "DST",
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        {
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          "intron_rank": 12,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1266-261C>T",
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          "transcript": "NM_001144770.2",
          "protein_id": "NP_001138242.1",
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          "cdna_start": null,
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          "mane_select": null,
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          "feature": null
        },
        {
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          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 95,
          "intron_rank": 12,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1266-261C>T",
          "hgvs_p": null,
          "transcript": "ENST00000312431.10",
          "protein_id": "ENSP00000307959.7",
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          "aa_start": null,
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          "cdna_start": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "exon_count": 94,
          "intron_rank": 11,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1146-261C>T",
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          "protein_id": "NP_899236.1",
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        {
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          "exon_count": 94,
          "intron_rank": 11,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1146-261C>T",
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          "transcript": "ENST00000421834.7",
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        },
        {
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 93,
          "intron_rank": 11,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1146-261C>T",
          "hgvs_p": null,
          "transcript": "NM_001386100.1",
          "protein_id": "NP_001373029.1",
          "transcript_support_level": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 17987,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 93,
          "intron_rank": 12,
          "intron_rank_end": null,
          "gene_symbol": "DST",
          "gene_hgnc_id": 1090,
          "hgvs_c": "c.1266-261C>T",
          "hgvs_p": null,
          "transcript": "ENST00000520645.6",
          "protein_id": "ENSP00000431030.2",
          "transcript_support_level": 2,
          "aa_start": null,
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      ],
      "gene_symbol": "DST",
      "gene_hgnc_id": 1090,
      "dbsnp": "rs75671065",
      "frequency_reference_population": 0.0023190773,
      "hom_count_reference_population": 18,
      "allele_count_reference_population": 3743,
      "gnomad_exomes_af": 0.00233692,
      "gnomad_genomes_af": 0.00214776,
      "gnomad_exomes_ac": 3416,
      "gnomad_genomes_ac": 327,
      "gnomad_exomes_homalt": 16,
      "gnomad_genomes_homalt": 2,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.00861629843711853,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.131,
      "revel_prediction": "Benign",
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.2,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 3.229,
      "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": -13,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -13,
          "benign_score": 13,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000680361.1",
          "gene_symbol": "DST",
          "hgnc_id": 1090,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1779-261C>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " localized or generalized intermediate, with BP230 deficiency,Epidermolysis bullosa simplex 3,Hereditary sensory and autonomic neuropathy type 6,Multiple sclerosis,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:1 LB:2 B:1",
      "phenotype_combined": "Hereditary sensory and autonomic neuropathy type 6|Hereditary sensory and autonomic neuropathy type 6;Epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency|not provided|Multiple sclerosis",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}