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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: 4-119513249-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=119513249&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 119513249,
      "ref": "T",
      "alt": "C",
      "effect": "intron_variant",
      "transcript": "ENST00000354960.8",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "PDE5A",
          "gene_hgnc_id": 8784,
          "hgvs_c": "c.2001-2115A>G",
          "hgvs_p": null,
          "transcript": "NM_001083.4",
          "protein_id": "NP_001074.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 875,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2628,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6959,
          "mane_select": "ENST00000354960.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "PDE5A",
          "gene_hgnc_id": 8784,
          "hgvs_c": "c.2001-2115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000354960.8",
          "protein_id": "ENSP00000347046.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 875,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2628,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6959,
          "mane_select": "NM_001083.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "PDE5A",
          "gene_hgnc_id": 8784,
          "hgvs_c": "c.1875-2115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000264805.9",
          "protein_id": "ENSP00000264805.5",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 833,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2502,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3020,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000291203",
          "gene_hgnc_id": null,
          "hgvs_c": "n.200+329T>C",
          "hgvs_p": null,
          "transcript": "ENST00000500559.6",
          "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": 453,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "PDE5A",
          "gene_hgnc_id": 8784,
          "hgvs_c": "c.1875-2115A>G",
          "hgvs_p": null,
          "transcript": "NM_033430.3",
          "protein_id": "NP_236914.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 833,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2502,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 7262,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "PDE5A",
          "gene_hgnc_id": 8784,
          "hgvs_c": "c.1845-2115A>G",
          "hgvs_p": null,
          "transcript": "NM_033437.4",
          "protein_id": "NP_246273.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 823,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2472,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6720,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": 14,
          "intron_rank_end": null,
          "gene_symbol": "PDE5A",
          "gene_hgnc_id": 8784,
          "hgvs_c": "c.1845-2115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000394439.5",
          "protein_id": "ENSP00000377957.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 823,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2472,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6770,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PDE5A",
          "gene_hgnc_id": 8784,
          "hgvs_c": "c.54-2115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000503412.1",
          "protein_id": "ENSP00000425810.1",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 184,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 555,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 892,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000291203",
          "gene_hgnc_id": null,
          "hgvs_c": "n.636+279T>C",
          "hgvs_p": null,
          "transcript": "ENST00000498873.5",
          "protein_id": null,
          "transcript_support_level": 5,
          "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": 981,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": 10,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000291203",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1203+279T>C",
          "hgvs_p": null,
          "transcript": "ENST00000508519.6",
          "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,
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          "cdna_length": 1361,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PDE5A",
          "gene_hgnc_id": 8784,
          "hgvs_c": "n.599-2115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000509612.1",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 738,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
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          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 5,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000291203",
          "gene_hgnc_id": null,
          "hgvs_c": "n.463+279T>C",
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          "transcript": "ENST00000510844.5",
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        {
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          "canonical": false,
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          "strand": true,
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          "intron_rank": 11,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000291203",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1318+279T>C",
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          "transcript": "ENST00000685525.2",
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        {
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          "hgvs_c": "n.1225+279T>C",
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          "transcript": "ENST00000685974.2",
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        },
        {
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          "gene_symbol": "ENSG00000291203",
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          "hgvs_c": "n.1290+279T>C",
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          "intron_rank": 10,
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          "gene_symbol": "ENSG00000291203",
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          "hgvs_c": "n.1279+279T>C",
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          "transcript": "ENST00000688480.2",
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          "exon_rank": null,
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          "exon_count": 11,
          "intron_rank": 10,
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          "gene_symbol": "ENSG00000291203",
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          "hgvs_c": "n.1219+329T>C",
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        {
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          "exon_count": 12,
          "intron_rank": 10,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000291203",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1256+279T>C",
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          "transcript": "ENST00000692945.1",
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      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.8999999761581421,
      "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": -0.9,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -2.241,
      "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": -2,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PM2,BP4_Strong",
      "acmg_by_gene": [
        {
          "score": -2,
          "benign_score": 4,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000354960.8",
          "gene_symbol": "PDE5A",
          "hgnc_id": 8784,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.2001-2115A>G",
          "hgvs_p": null
        },
        {
          "score": -2,
          "benign_score": 4,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000500559.6",
          "gene_symbol": "ENSG00000291203",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.200+329T>C",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}