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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: 5-78116244-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=78116244&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "5",
      "pos": 78116244,
      "ref": "C",
      "alt": "T",
      "effect": "intron_variant",
      "transcript": "ENST00000255194.11",
      "consequences": [
        {
          "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": 27,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1969-10G>A",
          "hgvs_p": null,
          "transcript": "NM_003664.5",
          "protein_id": "NP_003655.3",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1094,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3285,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3980,
          "mane_select": "ENST00000255194.11",
          "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": 27,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1969-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000255194.11",
          "protein_id": "ENSP00000255194.7",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1094,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3285,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3980,
          "mane_select": "NM_003664.5",
          "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": 27,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1822-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000519295.7",
          "protein_id": "ENSP00000430597.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1045,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3138,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 14714,
          "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": 26,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1969-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000695515.1",
          "protein_id": "ENSP00000511978.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1055,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3168,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3744,
          "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": 28,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1969-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000695511.1",
          "protein_id": "ENSP00000511974.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1053,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3162,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4045,
          "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": 28,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1963-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000695454.1",
          "protein_id": "ENSP00000511922.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1051,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3156,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4064,
          "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": 27,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1834-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000695513.1",
          "protein_id": "ENSP00000511976.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1049,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3150,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3973,
          "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": 27,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1822-10G>A",
          "hgvs_p": null,
          "transcript": "NM_001271769.2",
          "protein_id": "NP_001258698.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1045,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3138,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5796,
          "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": 28,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1912-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000695453.1",
          "protein_id": "ENSP00000511921.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1034,
          "cds_start": -4,
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          "cds_length": 3105,
          "cdna_start": null,
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          "cdna_length": 3977,
          "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": 25,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "c.1969-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000695512.1",
          "protein_id": "ENSP00000511975.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 1034,
          "cds_start": -4,
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          "cdna_start": null,
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          "mane_select": null,
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        {
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          "canonical": false,
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          "exon_count": 26,
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          "gene_symbol": "AP3B1",
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          "hgvs_c": "c.1969-10G>A",
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          "cds_start": -4,
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          "cdna_start": null,
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          "mane_select": null,
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        {
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          "intron_rank": 17,
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          "gene_symbol": "AP3B1",
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          "hgvs_c": "c.1969-10G>A",
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          "gene_symbol": "AP3B1",
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          "gene_symbol": "AP3B1",
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        {
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        {
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          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
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          "transcript": "ENST00000695488.1",
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          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4042,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "n.2127-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000695505.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 4765,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": 17,
          "intron_rank_end": null,
          "gene_symbol": "AP3B1",
          "gene_hgnc_id": 566,
          "hgvs_c": "n.1969-10G>A",
          "hgvs_p": null,
          "transcript": "ENST00000695507.1",
          "protein_id": "ENSP00000511970.1",
          "transcript_support_level": null,
          "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": 4108,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "AP3B1",
      "gene_hgnc_id": 566,
      "dbsnp": "rs77009095",
      "frequency_reference_population": 0.069233194,
      "hom_count_reference_population": 4256,
      "allele_count_reference_population": 110353,
      "gnomad_exomes_af": 0.0709428,
      "gnomad_genomes_af": 0.0530393,
      "gnomad_exomes_ac": 102280,
      "gnomad_genomes_ac": 8073,
      "gnomad_exomes_homalt": 3930,
      "gnomad_genomes_homalt": 326,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.6100000143051147,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0.15199999511241913,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "dbscSNV1_RF",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.61,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.179,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": 0.000365887800970999,
      "dbscsnv_ada_prediction": "Benign",
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -20,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
      "acmg_by_gene": [
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000255194.11",
          "gene_symbol": "AP3B1",
          "hgnc_id": 566,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1969-10G>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Hermansky-Pudlak syndrome,Hermansky-Pudlak syndrome 2,not provided,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2 B:4",
      "phenotype_combined": "not specified|Hermansky-Pudlak syndrome|not provided|Hermansky-Pudlak syndrome 2",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}