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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: 4-121854706-CCTCT-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=121854706&ref=CCTCT&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 121854706,
      "ref": "CCTCT",
      "alt": "C",
      "effect": "frameshift_variant",
      "transcript": "ENST00000264499.9",
      "consequences": [
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.712_715delAGAG",
          "hgvs_p": "p.Arg238fs",
          "transcript": "NM_176824.3",
          "protein_id": "NP_789794.1",
          "transcript_support_level": null,
          "aa_start": 238,
          "aa_end": null,
          "aa_length": 715,
          "cds_start": 712,
          "cds_end": null,
          "cds_length": 2148,
          "cdna_start": 876,
          "cdna_end": null,
          "cdna_length": 3840,
          "mane_select": "ENST00000264499.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.712_715delAGAG",
          "hgvs_p": "p.Arg238fs",
          "transcript": "ENST00000264499.9",
          "protein_id": "ENSP00000264499.4",
          "transcript_support_level": 1,
          "aa_start": 238,
          "aa_end": null,
          "aa_length": 715,
          "cds_start": 712,
          "cds_end": null,
          "cds_length": 2148,
          "cdna_start": 876,
          "cdna_end": null,
          "cdna_length": 3840,
          "mane_select": "NM_176824.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.712_715delAGAG",
          "hgvs_p": "p.Arg238fs",
          "transcript": "ENST00000506636.1",
          "protein_id": "ENSP00000423626.1",
          "transcript_support_level": 1,
          "aa_start": 238,
          "aa_end": null,
          "aa_length": 672,
          "cds_start": 712,
          "cds_end": null,
          "cds_length": 2019,
          "cdna_start": 852,
          "cdna_end": null,
          "cdna_length": 2570,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.712_715delAGAG",
          "hgvs_p": "p.Arg238fs",
          "transcript": "NM_018190.4",
          "protein_id": "NP_060660.2",
          "transcript_support_level": null,
          "aa_start": 238,
          "aa_end": null,
          "aa_length": 672,
          "cds_start": 712,
          "cds_end": null,
          "cds_length": 2019,
          "cdna_start": 876,
          "cdna_end": null,
          "cdna_length": 2594,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.760_763delAGAG",
          "hgvs_p": "p.Arg254fs",
          "transcript": "XM_011532079.4",
          "protein_id": "XP_011530381.1",
          "transcript_support_level": null,
          "aa_start": 254,
          "aa_end": null,
          "aa_length": 731,
          "cds_start": 760,
          "cds_end": null,
          "cds_length": 2196,
          "cdna_start": 924,
          "cdna_end": null,
          "cdna_length": 3888,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.757_760delAGAG",
          "hgvs_p": "p.Arg253fs",
          "transcript": "XM_011532080.4",
          "protein_id": "XP_011530382.1",
          "transcript_support_level": null,
          "aa_start": 253,
          "aa_end": null,
          "aa_length": 730,
          "cds_start": 757,
          "cds_end": null,
          "cds_length": 2193,
          "cdna_start": 921,
          "cdna_end": null,
          "cdna_length": 3885,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.715_718delAGAG",
          "hgvs_p": "p.Arg239fs",
          "transcript": "XM_005263106.5",
          "protein_id": "XP_005263163.1",
          "transcript_support_level": null,
          "aa_start": 239,
          "aa_end": null,
          "aa_length": 716,
          "cds_start": 715,
          "cds_end": null,
          "cds_length": 2151,
          "cdna_start": 879,
          "cdna_end": null,
          "cdna_length": 3843,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.760_763delAGAG",
          "hgvs_p": "p.Arg254fs",
          "transcript": "XM_011532081.4",
          "protein_id": "XP_011530383.1",
          "transcript_support_level": null,
          "aa_start": 254,
          "aa_end": null,
          "aa_length": 676,
          "cds_start": 760,
          "cds_end": null,
          "cds_length": 2031,
          "cdna_start": 924,
          "cdna_end": null,
          "cdna_length": 3723,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.757_760delAGAG",
          "hgvs_p": "p.Arg253fs",
          "transcript": "XM_047415889.1",
          "protein_id": "XP_047271845.1",
          "transcript_support_level": null,
          "aa_start": 253,
          "aa_end": null,
          "aa_length": 675,
          "cds_start": 757,
          "cds_end": null,
          "cds_length": 2028,
          "cdna_start": 921,
          "cdna_end": null,
          "cdna_length": 3720,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.715_718delAGAG",
          "hgvs_p": "p.Arg239fs",
          "transcript": "XM_047415890.1",
          "protein_id": "XP_047271846.1",
          "transcript_support_level": null,
          "aa_start": 239,
          "aa_end": null,
          "aa_length": 661,
          "cds_start": 715,
          "cds_end": null,
          "cds_length": 1986,
          "cdna_start": 879,
          "cdna_end": null,
          "cdna_length": 3678,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RG",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS7",
          "gene_hgnc_id": 18758,
          "hgvs_c": "c.712_715delAGAG",
          "hgvs_p": "p.Arg238fs",
          "transcript": "XM_017008357.3",
          "protein_id": "XP_016863846.1",
          "transcript_support_level": null,
          "aa_start": 238,
          "aa_end": null,
          "aa_length": 660,
          "cds_start": 712,
          "cds_end": null,
          "cds_length": 1983,
          "cdna_start": 876,
          "cdna_end": null,
          "cdna_length": 3675,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "BBS7",
      "gene_hgnc_id": 18758,
      "dbsnp": "rs760165634",
      "frequency_reference_population": 0.000042204727,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 68,
      "gnomad_exomes_af": 0.000041805,
      "gnomad_genomes_af": 0.0000460411,
      "gnomad_exomes_ac": 61,
      "gnomad_genomes_ac": 7,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "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": 7.251,
      "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": 18,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 18,
          "benign_score": 0,
          "pathogenic_score": 18,
          "criteria": [
            "PVS1",
            "PM2",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000264499.9",
          "gene_symbol": "BBS7",
          "hgnc_id": 18758,
          "effects": [
            "frameshift_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.712_715delAGAG",
          "hgvs_p": "p.Arg238fs"
        }
      ],
      "clinvar_disease": "BBS7-related disorder,Bardet-Biedl syndrome,Bardet-Biedl syndrome 1,Bardet-Biedl syndrome 7,Retinal dystrophy,not provided",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:15",
      "phenotype_combined": "not provided|Bardet-Biedl syndrome|Retinal dystrophy|Bardet-Biedl syndrome 7|Bardet-Biedl syndrome 1|BBS7-related disorder",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}