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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: 13-26215577-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=26215577&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "13",
      "pos": 26215577,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000381588.9",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "NM_005977.4",
          "protein_id": "NP_005968.1",
          "transcript_support_level": null,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 685,
          "cds_start": 305,
          "cds_end": null,
          "cds_length": 2058,
          "cdna_start": 718,
          "cdna_end": null,
          "cdna_length": 3520,
          "mane_select": "ENST00000381588.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "ENST00000381588.9",
          "protein_id": "ENSP00000371000.4",
          "transcript_support_level": 1,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 685,
          "cds_start": 305,
          "cds_end": null,
          "cds_length": 2058,
          "cdna_start": 718,
          "cdna_end": null,
          "cdna_length": 3520,
          "mane_select": "NM_005977.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "ENST00000346166.7",
          "protein_id": "ENSP00000342121.3",
          "transcript_support_level": 1,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 685,
          "cds_start": 305,
          "cds_end": null,
          "cds_length": 2058,
          "cdna_start": 467,
          "cdna_end": null,
          "cdna_length": 3282,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "ENST00000381570.7",
          "protein_id": "ENSP00000370982.3",
          "transcript_support_level": 1,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 685,
          "cds_start": 305,
          "cds_end": null,
          "cds_length": 2058,
          "cdna_start": 596,
          "cdna_end": null,
          "cdna_length": 3398,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "n.665G>A",
          "hgvs_p": null,
          "transcript": "ENST00000468480.5",
          "protein_id": null,
          "transcript_support_level": 1,
          "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": 1105,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "NM_183043.3",
          "protein_id": "NP_898864.1",
          "transcript_support_level": null,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 685,
          "cds_start": 305,
          "cds_end": null,
          "cds_length": 2058,
          "cdna_start": 939,
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          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "NM_183044.3",
          "protein_id": "NP_898865.1",
          "transcript_support_level": null,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 685,
          "cds_start": 305,
          "cds_end": null,
          "cds_length": 2058,
          "cdna_start": 735,
          "cdna_end": null,
          "cdna_length": 3537,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "NM_183045.1",
          "protein_id": "NP_898866.1",
          "transcript_support_level": null,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 142,
          "cds_start": 305,
          "cds_end": null,
          "cds_length": 429,
          "cdna_start": 775,
          "cdna_end": null,
          "cdna_length": 1215,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
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          "exon_count": 5,
          "intron_rank": null,
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          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "XM_005266485.4",
          "protein_id": "XP_005266542.1",
          "transcript_support_level": null,
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          "mane_select": null,
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        {
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          "consequences": [
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          "exon_rank": 5,
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          "exon_count": 5,
          "intron_rank": null,
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          "gene_symbol": "RNF6",
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          "hgvs_c": "c.305G>A",
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          "transcript": "XM_005266486.3",
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          "cdna_start": 886,
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        },
        {
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          "exon_count": 6,
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          "hgvs_p": "p.Arg102Lys",
          "transcript": "XM_047430499.1",
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        },
        {
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          ],
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          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys",
          "transcript": "XM_047430500.1",
          "protein_id": "XP_047286456.1",
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        },
        {
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          "protein_coding": false,
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          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 5,
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          "exon_count": 5,
          "intron_rank": null,
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          "gene_symbol": "RNF6",
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          "hgvs_c": "n.417G>A",
          "hgvs_p": null,
          "transcript": "ENST00000498039.5",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cdna_length": 855,
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        },
        {
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          "protein_coding": true,
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          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 2,
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          "exon_count": 3,
          "intron_rank": null,
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          "gene_symbol": "RNF6",
          "gene_hgnc_id": 10069,
          "hgvs_c": "c.-60G>A",
          "hgvs_p": null,
          "transcript": "XM_047430494.1",
          "protein_id": "XP_047286450.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "cds_start": -4,
          "cds_end": null,
          "cds_length": 990,
          "cdna_start": null,
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          "cdna_length": 2210,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
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        }
      ],
      "gene_symbol": "RNF6",
      "gene_hgnc_id": 10069,
      "dbsnp": "rs121434522",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.08092328906059265,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.029999999329447746,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.045,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0876,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.55,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.853,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.03,
      "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": 2,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP5,BP4",
      "acmg_by_gene": [
        {
          "score": 2,
          "benign_score": 1,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP5",
            "BP4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000381588.9",
          "gene_symbol": "RNF6",
          "hgnc_id": 10069,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "Unknown",
          "hgvs_c": "c.305G>A",
          "hgvs_p": "p.Arg102Lys"
        }
      ],
      "clinvar_disease": " somatic,Esophageal squamous cell carcinoma",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "no assertion criteria provided",
      "clinvar_submissions_summary": "null",
      "phenotype_combined": "Esophageal squamous cell carcinoma, somatic",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}