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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: 19-50409146-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=50409146&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "19",
      "pos": 50409146,
      "ref": "G",
      "alt": "A",
      "effect": "synonymous_variant",
      "transcript": "ENST00000440232.7",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "NM_002691.4",
          "protein_id": "NP_002682.2",
          "transcript_support_level": null,
          "aa_start": 639,
          "aa_end": null,
          "aa_length": 1107,
          "cds_start": 1917,
          "cds_end": null,
          "cds_length": 3324,
          "cdna_start": 1962,
          "cdna_end": null,
          "cdna_length": 3436,
          "mane_select": "ENST00000440232.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "ENST00000440232.7",
          "protein_id": "ENSP00000406046.1",
          "transcript_support_level": 1,
          "aa_start": 639,
          "aa_end": null,
          "aa_length": 1107,
          "cds_start": 1917,
          "cds_end": null,
          "cds_length": 3324,
          "cdna_start": 1962,
          "cdna_end": null,
          "cdna_length": 3436,
          "mane_select": "NM_002691.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1995G>A",
          "hgvs_p": "p.Arg665Arg",
          "transcript": "ENST00000595904.6",
          "protein_id": "ENSP00000472445.1",
          "transcript_support_level": 1,
          "aa_start": 665,
          "aa_end": null,
          "aa_length": 1133,
          "cds_start": 1995,
          "cds_end": null,
          "cds_length": 3402,
          "cdna_start": 2040,
          "cdna_end": null,
          "cdna_length": 3514,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "ENST00000599857.7",
          "protein_id": "ENSP00000473052.1",
          "transcript_support_level": 1,
          "aa_start": 639,
          "aa_end": null,
          "aa_length": 1107,
          "cds_start": 1917,
          "cds_end": null,
          "cds_length": 3324,
          "cdna_start": 1989,
          "cdna_end": null,
          "cdna_length": 3467,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1995G>A",
          "hgvs_p": "p.Arg665Arg",
          "transcript": "NM_001308632.1",
          "protein_id": "NP_001295561.1",
          "transcript_support_level": null,
          "aa_start": 665,
          "aa_end": null,
          "aa_length": 1133,
          "cds_start": 1995,
          "cds_end": null,
          "cds_length": 3402,
          "cdna_start": 1995,
          "cdna_end": null,
          "cdna_length": 3473,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1995G>A",
          "hgvs_p": "p.Arg665Arg",
          "transcript": "ENST00000644560.2",
          "protein_id": "ENSP00000495618.2",
          "transcript_support_level": null,
          "aa_start": 665,
          "aa_end": null,
          "aa_length": 1109,
          "cds_start": 1995,
          "cds_end": null,
          "cds_length": 3330,
          "cdna_start": 1995,
          "cdna_end": null,
          "cdna_length": 3370,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "NM_001256849.1",
          "protein_id": "NP_001243778.1",
          "transcript_support_level": null,
          "aa_start": 639,
          "aa_end": null,
          "aa_length": 1107,
          "cds_start": 1917,
          "cds_end": null,
          "cds_length": 3324,
          "cdna_start": 1989,
          "cdna_end": null,
          "cdna_length": 3467,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "NM_001438212.1",
          "protein_id": "NP_001425141.1",
          "transcript_support_level": null,
          "aa_start": 639,
          "aa_end": null,
          "aa_length": 1107,
          "cds_start": 1917,
          "cds_end": null,
          "cds_length": 3324,
          "cdna_start": 2107,
          "cdna_end": null,
          "cdna_length": 3581,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "NM_001438213.1",
          "protein_id": "NP_001425142.1",
          "transcript_support_level": null,
          "aa_start": 639,
          "aa_end": null,
          "aa_length": 1107,
          "cds_start": 1917,
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          "cds_length": 3324,
          "cdna_start": 2088,
          "cdna_end": null,
          "cdna_length": 3562,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "ENST00000593887.2",
          "protein_id": "ENSP00000472607.2",
          "transcript_support_level": 5,
          "aa_start": 639,
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          "cdna_start": 2296,
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        {
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          ],
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          "gene_symbol": "POLD1",
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          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "ENST00000601098.6",
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          "mane_select": null,
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        },
        {
          "aa_ref": "R",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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        {
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          "strand": true,
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          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "NM_001438210.1",
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        {
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          "consequences": [
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          ],
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          "gene_symbol": "POLD1",
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          "hgvs_c": "c.1917G>A",
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          "transcript": "NM_001438211.1",
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        {
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        {
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          "gene_symbol": "POLD1",
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          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg",
          "transcript": "XM_011527038.2",
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        {
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          "gene_symbol": "POLD1",
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          "hgvs_c": "c.1917G>A",
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          "transcript": "XM_047438950.1",
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
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          "intron_rank": null,
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          "gene_symbol": "POLD1",
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          "transcript_support_level": 5,
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        },
        {
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          "protein_coding": false,
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          "consequences": [
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          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
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          "gene_symbol": "POLD1",
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          "hgvs_c": "n.1917G>A",
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          "protein_id": "ENSP00000470726.1",
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        },
        {
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          "protein_coding": false,
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          "consequences": [
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          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
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          "gene_symbol": "POLD1",
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          "hgvs_c": "n.1917G>A",
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          "protein_id": "ENSP00000496078.1",
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        },
        {
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 16,
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          "exon_count": 26,
          "intron_rank": null,
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          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "n.1962G>A",
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          "transcript": "NR_046402.2",
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          "transcript_support_level": null,
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          "cdna_length": 3333,
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        },
        {
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          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLD1",
          "gene_hgnc_id": 9175,
          "hgvs_c": "n.1986G>A",
          "hgvs_p": null,
          "transcript": "XR_935835.3",
          "protein_id": null,
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          "aa_length": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 2395,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "POLD1",
      "gene_hgnc_id": 9175,
      "dbsnp": "rs1334171687",
      "frequency_reference_population": 0.000006568576,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": 0.00000656858,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.33000001311302185,
      "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": -0.33,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 3.185,
      "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": -9,
      "acmg_classification": "Benign",
      "acmg_criteria": "PM2,BP4_Moderate,BP6_Very_Strong,BP7",
      "acmg_by_gene": [
        {
          "score": -9,
          "benign_score": 11,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Moderate",
            "BP6_Very_Strong",
            "BP7"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000440232.7",
          "gene_symbol": "POLD1",
          "hgnc_id": 9175,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.1917G>A",
          "hgvs_p": "p.Arg639Arg"
        }
      ],
      "clinvar_disease": " 10, susceptibility to,Colorectal cancer,Hereditary cancer-predisposing syndrome",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2",
      "phenotype_combined": "Colorectal cancer, susceptibility to, 10|Hereditary cancer-predisposing syndrome",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}