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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: 8-100240660-A-AG (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=100240660&ref=A&alt=AG&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "8",
      "pos": 100240660,
      "ref": "A",
      "alt": "AG",
      "effect": "frameshift_variant",
      "transcript": "ENST00000388798.7",
      "consequences": [
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2542dupG",
          "hgvs_p": "p.Asp848fs",
          "transcript": "NM_003114.5",
          "protein_id": "NP_003105.2",
          "transcript_support_level": null,
          "aa_start": 848,
          "aa_end": null,
          "aa_length": 926,
          "cds_start": 2543,
          "cds_end": null,
          "cds_length": 2781,
          "cdna_start": 2575,
          "cdna_end": null,
          "cdna_length": 3695,
          "mane_select": "ENST00000388798.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2542dupG",
          "hgvs_p": "p.Asp848fs",
          "transcript": "ENST00000388798.7",
          "protein_id": "ENSP00000373450.3",
          "transcript_support_level": 1,
          "aa_start": 848,
          "aa_end": null,
          "aa_length": 926,
          "cds_start": 2543,
          "cds_end": null,
          "cds_length": 2781,
          "cdna_start": 2575,
          "cdna_end": null,
          "cdna_length": 3695,
          "mane_select": "NM_003114.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2542dupG",
          "hgvs_p": "p.Asp848fs",
          "transcript": "NM_001374321.1",
          "protein_id": "NP_001361250.1",
          "transcript_support_level": null,
          "aa_start": 848,
          "aa_end": null,
          "aa_length": 926,
          "cds_start": 2543,
          "cds_end": null,
          "cds_length": 2781,
          "cdna_start": 2636,
          "cdna_end": null,
          "cdna_length": 3756,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2542dupG",
          "hgvs_p": "p.Asp848fs",
          "transcript": "NM_172218.3",
          "protein_id": "NP_757367.1",
          "transcript_support_level": null,
          "aa_start": 848,
          "aa_end": null,
          "aa_length": 926,
          "cds_start": 2543,
          "cds_end": null,
          "cds_length": 2781,
          "cdna_start": 2626,
          "cdna_end": null,
          "cdna_length": 3746,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2542dupG",
          "hgvs_p": "p.Asp848fs",
          "transcript": "ENST00000251809.4",
          "protein_id": "ENSP00000251809.3",
          "transcript_support_level": 5,
          "aa_start": 848,
          "aa_end": null,
          "aa_length": 926,
          "cds_start": 2543,
          "cds_end": null,
          "cds_length": 2781,
          "cdna_start": 2629,
          "cdna_end": null,
          "cdna_length": 3748,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2542dupG",
          "hgvs_p": "p.Asp848fs",
          "transcript": "XM_011517243.3",
          "protein_id": "XP_011515545.1",
          "transcript_support_level": null,
          "aa_start": 848,
          "aa_end": null,
          "aa_length": 926,
          "cds_start": 2543,
          "cds_end": null,
          "cds_length": 2781,
          "cdna_start": 2998,
          "cdna_end": null,
          "cdna_length": 4118,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2542dupG",
          "hgvs_p": "p.Asp848fs",
          "transcript": "XM_047422128.1",
          "protein_id": "XP_047278084.1",
          "transcript_support_level": null,
          "aa_start": 848,
          "aa_end": null,
          "aa_length": 926,
          "cds_start": 2543,
          "cds_end": null,
          "cds_length": 2781,
          "cdna_start": 2708,
          "cdna_end": null,
          "cdna_length": 3828,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2389dupG",
          "hgvs_p": "p.Asp797fs",
          "transcript": "XM_011517240.3",
          "protein_id": "XP_011515542.1",
          "transcript_support_level": null,
          "aa_start": 797,
          "aa_end": null,
          "aa_length": 875,
          "cds_start": 2390,
          "cds_end": null,
          "cds_length": 2628,
          "cdna_start": 2473,
          "cdna_end": null,
          "cdna_length": 3593,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G?",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "c.2377dupG",
          "hgvs_p": "p.Asp793fs",
          "transcript": "XM_011517241.3",
          "protein_id": "XP_011515543.1",
          "transcript_support_level": null,
          "aa_start": 793,
          "aa_end": null,
          "aa_length": 871,
          "cds_start": 2378,
          "cds_end": null,
          "cds_length": 2616,
          "cdna_start": 2461,
          "cdna_end": null,
          "cdna_length": 3581,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "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": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "n.106dupG",
          "hgvs_p": null,
          "transcript": "ENST00000519409.1",
          "protein_id": null,
          "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": 450,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SPAG1",
          "gene_hgnc_id": 11212,
          "hgvs_c": "n.*145_*146insG",
          "hgvs_p": null,
          "transcript": "ENST00000519424.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": 645,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "SPAG1",
      "gene_hgnc_id": 11212,
      "dbsnp": "rs886037653",
      "frequency_reference_population": 6.8406e-7,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": 6.8406e-7,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": null,
      "computational_prediction_selected": null,
      "computational_source_selected": null,
      "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": null,
      "bayesdelnoaf_prediction": null,
      "phylop100way_score": 6.829,
      "phylop100way_prediction": "Uncertain_significance",
      "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": 10,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PVS1,PM2",
      "acmg_by_gene": [
        {
          "score": 10,
          "benign_score": 0,
          "pathogenic_score": 10,
          "criteria": [
            "PVS1",
            "PM2"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000388798.7",
          "gene_symbol": "SPAG1",
          "hgnc_id": 11212,
          "effects": [
            "frameshift_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.2542dupG",
          "hgvs_p": "p.Asp848fs"
        }
      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}