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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: 3-129440351-G-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=129440351&ref=G&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 129440351,
      "ref": "G",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "ENST00000348417.7",
      "consequences": [
        {
          "aa_ref": "W",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "NM_052989.3",
          "protein_id": "NP_443715.1",
          "transcript_support_level": null,
          "aa_start": 7,
          "aa_end": null,
          "aa_length": 1241,
          "cds_start": 21,
          "cds_end": null,
          "cds_length": 3726,
          "cdna_start": 128,
          "cdna_end": null,
          "cdna_length": 4075,
          "mane_select": "ENST00000348417.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "ENST00000348417.7",
          "protein_id": "ENSP00000324005.4",
          "transcript_support_level": 1,
          "aa_start": 7,
          "aa_end": null,
          "aa_length": 1241,
          "cds_start": 21,
          "cds_end": null,
          "cds_length": 3726,
          "cdna_start": 128,
          "cdna_end": null,
          "cdna_length": 4075,
          "mane_select": "NM_052989.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "ENST00000296266.7",
          "protein_id": "ENSP00000296266.3",
          "transcript_support_level": 1,
          "aa_start": 7,
          "aa_end": null,
          "aa_length": 1292,
          "cds_start": 21,
          "cds_end": null,
          "cds_length": 3879,
          "cdna_start": 213,
          "cdna_end": null,
          "cdna_length": 4151,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "ENST00000507564.5",
          "protein_id": "ENSP00000425536.1",
          "transcript_support_level": 1,
          "aa_start": 7,
          "aa_end": null,
          "aa_length": 1234,
          "cds_start": 21,
          "cds_end": null,
          "cds_length": 3705,
          "cdna_start": 140,
          "cdna_end": null,
          "cdna_length": 3824,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "ENST00000347300.6",
          "protein_id": "ENSP00000323973.3",
          "transcript_support_level": 1,
          "aa_start": 7,
          "aa_end": null,
          "aa_length": 1182,
          "cds_start": 21,
          "cds_end": null,
          "cds_length": 3549,
          "cdna_start": 227,
          "cdna_end": null,
          "cdna_length": 3841,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "ENST00000349441.6",
          "protein_id": "ENSP00000324165.3",
          "transcript_support_level": 1,
          "aa_start": 7,
          "aa_end": null,
          "aa_length": 1131,
          "cds_start": 21,
          "cds_end": null,
          "cds_length": 3396,
          "cdna_start": 108,
          "cdna_end": null,
          "cdna_length": 3569,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "NM_052985.4",
          "protein_id": "NP_443711.2",
          "transcript_support_level": null,
          "aa_start": 7,
          "aa_end": null,
          "aa_length": 1292,
          "cds_start": 21,
          "cds_end": null,
          "cds_length": 3879,
          "cdna_start": 128,
          "cdna_end": null,
          "cdna_length": 4228,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "ENST00000689643.1",
          "protein_id": "ENSP00000509801.1",
          "transcript_support_level": null,
          "aa_start": 7,
          "aa_end": null,
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          "cds_start": 21,
          "cds_end": null,
          "cds_length": 3798,
          "cdna_start": 225,
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          "cdna_length": 4030,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
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          "protein_coding": true,
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          ],
          "exon_rank": 1,
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          "intron_rank": null,
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          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.21G>C",
          "hgvs_p": "p.Trp7Cys",
          "transcript": "NM_001410808.1",
          "protein_id": "NP_001397737.1",
          "transcript_support_level": null,
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        {
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          "gene_symbol": "IFT122",
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          "hgvs_p": "p.Trp7Cys",
          "transcript": "ENST00000692242.1",
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      "dbsnp": "rs267607193",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
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      "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": 0.6140058040618896,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.467,
      "revel_prediction": "Uncertain_significance",
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      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.29,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 6.068,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0,
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      "apogee2_score": null,
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      "acmg_score": 3,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP5",
      "acmg_by_gene": [
        {
          "score": 3,
          "benign_score": 0,
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            "PP5"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000348417.7",
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          "hgnc_id": 13556,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
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        {
          "score": 3,
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          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000393278.6",
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          "effects": [
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          "inheritance_mode": "AD,AR",
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      ],
      "clinvar_disease": "Cranioectodermal dysplasia 1",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "no assertion criteria provided",
      "clinvar_submissions_summary": "O:1",
      "phenotype_combined": "Cranioectodermal dysplasia 1",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
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  ],
  "message": null
}