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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: 5-138772560-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=138772560&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "5",
      "pos": 138772560,
      "ref": "A",
      "alt": "G",
      "effect": "intron_variant",
      "transcript": "NM_001903.5",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001903.5",
          "protein_id": "NP_001894.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 906,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2721,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3754,
          "mane_select": "ENST00000302763.12",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "ENST00000302763.12",
          "protein_id": "ENSP00000304669.7",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 906,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2721,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3754,
          "mane_select": "NM_001903.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001323982.2",
          "protein_id": "NP_001310911.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 906,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2721,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4224,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001323983.1",
          "protein_id": "NP_001310912.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 906,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2721,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3945,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001323984.2",
          "protein_id": "NP_001310913.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 906,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2721,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3772,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001323985.2",
          "protein_id": "NP_001310914.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 897,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2694,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3727,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001323986.2",
          "protein_id": "NP_001310915.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 875,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2628,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3661,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001290307.3",
          "protein_id": "NP_001277236.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 841,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2526,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3825,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "ENST00000627109.2",
          "protein_id": "ENSP00000486200.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 841,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2526,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3831,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-115-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001290309.3",
          "protein_id": "NP_001277238.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 803,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2412,
          "cdna_start": null,
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          "cdna_length": 3558,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 18,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-208-9363A>G",
          "hgvs_p": null,
          "transcript": "NM_001290310.3",
          "protein_id": "NP_001277239.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 783,
          "cds_start": -4,
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          "cds_length": 2352,
          "cdna_start": null,
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          "cdna_length": 3591,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 6,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "ENST00000520158.5",
          "protein_id": "ENSP00000429457.1",
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          "aa_start": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "feature": null
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        {
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          "canonical": false,
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          "intron_rank": 1,
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          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-9+19050A>G",
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          "transcript": "ENST00000518910.5",
          "protein_id": "ENSP00000430626.1",
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          "aa_start": null,
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          "mane_select": null,
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        {
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          "exon_count": 4,
          "intron_rank": 1,
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          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
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          "transcript": "ENST00000523912.5",
          "protein_id": "ENSP00000430304.1",
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          "aa_start": null,
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          "cds_start": -4,
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          "mane_select": null,
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        },
        {
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          "gene_symbol": "CTNNA1",
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          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
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          "transcript": "ENST00000522227.5",
          "protein_id": "ENSP00000429636.1",
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          "mane_select": null,
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        {
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          "exon_count": 6,
          "intron_rank": 3,
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          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
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          "transcript": "ENST00000517980.5",
          "protein_id": "ENSP00000428439.1",
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        },
        {
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          "gene_symbol": "CTNNA1",
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          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "c.-2-9363A>G",
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        {
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          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "n.-2-9363A>G",
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          "transcript": "ENST00000519309.5",
          "protein_id": "ENSP00000430671.1",
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          "cdna_length": 869,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CTNNA1",
          "gene_hgnc_id": 2509,
          "hgvs_c": "n.-2-9363A>G",
          "hgvs_p": null,
          "transcript": "ENST00000521724.5",
          "protein_id": "ENSP00000431033.1",
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          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2741,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "CTNNA1",
      "gene_hgnc_id": 2509,
      "dbsnp": "rs148665639",
      "frequency_reference_population": 0.009019891,
      "hom_count_reference_population": 14,
      "allele_count_reference_population": 1374,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": 0.00901989,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": 1374,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": 14,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.5299999713897705,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.53,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.477,
      "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": "NM_001903.5",
          "gene_symbol": "CTNNA1",
          "hgnc_id": 2509,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.-2-9363A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Hereditary cancer-predisposing syndrome",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "no assertion criteria provided",
      "clinvar_submissions_summary": "null",
      "phenotype_combined": "Hereditary cancer-predisposing syndrome",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}