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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: 4-54290472-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=54290472&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 54290472,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_006206.6",
      "consequences": [
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDGFRA",
          "gene_hgnc_id": 8803,
          "hgvs_c": "c.3040G>A",
          "hgvs_p": "p.Ala1014Thr",
          "transcript": "NM_006206.6",
          "protein_id": "NP_006197.1",
          "transcript_support_level": null,
          "aa_start": 1014,
          "aa_end": null,
          "aa_length": 1089,
          "cds_start": 3040,
          "cds_end": null,
          "cds_length": 3270,
          "cdna_start": 3175,
          "cdna_end": null,
          "cdna_length": 6378,
          "mane_select": "ENST00000257290.10",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDGFRA",
          "gene_hgnc_id": 8803,
          "hgvs_c": "c.3040G>A",
          "hgvs_p": "p.Ala1014Thr",
          "transcript": "ENST00000257290.10",
          "protein_id": "ENSP00000257290.5",
          "transcript_support_level": 1,
          "aa_start": 1014,
          "aa_end": null,
          "aa_length": 1089,
          "cds_start": 3040,
          "cds_end": null,
          "cds_length": 3270,
          "cdna_start": 3175,
          "cdna_end": null,
          "cdna_length": 6378,
          "mane_select": "NM_006206.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000282278",
          "gene_hgnc_id": null,
          "hgvs_c": "c.2320G>A",
          "hgvs_p": "p.Ala774Thr",
          "transcript": "ENST00000507166.5",
          "protein_id": "ENSP00000423325.1",
          "transcript_support_level": 2,
          "aa_start": 774,
          "aa_end": null,
          "aa_length": 849,
          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 2550,
          "cdna_start": 2320,
          "cdna_end": null,
          "cdna_length": 2550,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDGFRA",
          "gene_hgnc_id": 8803,
          "hgvs_c": "c.3115G>A",
          "hgvs_p": "p.Ala1039Thr",
          "transcript": "NM_001347828.2",
          "protein_id": "NP_001334757.1",
          "transcript_support_level": null,
          "aa_start": 1039,
          "aa_end": null,
          "aa_length": 1114,
          "cds_start": 3115,
          "cds_end": null,
          "cds_length": 3345,
          "cdna_start": 3253,
          "cdna_end": null,
          "cdna_length": 6456,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDGFRA",
          "gene_hgnc_id": 8803,
          "hgvs_c": "c.3079G>A",
          "hgvs_p": "p.Ala1027Thr",
          "transcript": "NM_001347830.2",
          "protein_id": "NP_001334759.1",
          "transcript_support_level": null,
          "aa_start": 1027,
          "aa_end": null,
          "aa_length": 1102,
          "cds_start": 3079,
          "cds_end": null,
          "cds_length": 3309,
          "cdna_start": 3591,
          "cdna_end": null,
          "cdna_length": 6794,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDGFRA",
          "gene_hgnc_id": 8803,
          "hgvs_c": "c.3040G>A",
          "hgvs_p": "p.Ala1014Thr",
          "transcript": "NM_001347829.2",
          "protein_id": "NP_001334758.1",
          "transcript_support_level": null,
          "aa_start": 1014,
          "aa_end": null,
          "aa_length": 1089,
          "cds_start": 3040,
          "cds_end": null,
          "cds_length": 3270,
          "cdna_start": 3396,
          "cdna_end": null,
          "cdna_length": 6599,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDGFRA",
          "gene_hgnc_id": 8803,
          "hgvs_c": "c.3040G>A",
          "hgvs_p": "p.Ala1014Thr",
          "transcript": "XM_005265743.2",
          "protein_id": "XP_005265800.1",
          "transcript_support_level": null,
          "aa_start": 1014,
          "aa_end": null,
          "aa_length": 1089,
          "cds_start": 3040,
          "cds_end": null,
          "cds_length": 3270,
          "cdna_start": 3792,
          "cdna_end": null,
          "cdna_length": 6995,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDGFRA",
          "gene_hgnc_id": 8803,
          "hgvs_c": "c.3040G>A",
          "hgvs_p": "p.Ala1014Thr",
          "transcript": "XM_047415766.1",
          "protein_id": "XP_047271722.1",
          "transcript_support_level": null,
          "aa_start": 1014,
          "aa_end": null,
          "aa_length": 1089,
          "cds_start": 3040,
          "cds_end": null,
          "cds_length": 3270,
          "cdna_start": 3255,
          "cdna_end": null,
          "cdna_length": 6458,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PDGFRA",
          "gene_hgnc_id": 8803,
          "hgvs_c": "c.3040G>A",
          "hgvs_p": "p.Ala1014Thr",
          "transcript": "XM_047415767.1",
          "protein_id": "XP_047271723.1",
          "transcript_support_level": null,
          "aa_start": 1014,
          "aa_end": null,
          "aa_length": 1089,
          "cds_start": 3040,
          "cds_end": null,
          "cds_length": 3270,
          "cdna_start": 3558,
          "cdna_end": null,
          "cdna_length": 6761,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PDGFRA",
      "gene_hgnc_id": 8803,
      "dbsnp": "rs768291477",
      "frequency_reference_population": 0.000024171057,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 39,
      "gnomad_exomes_af": 0.0000246354,
      "gnomad_genomes_af": 0.0000197122,
      "gnomad_exomes_ac": 36,
      "gnomad_genomes_ac": 3,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.2135975956916809,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.267,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0887,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.45,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 5.768,
      "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": -7,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Moderate,BP6,BS2",
      "acmg_by_gene": [
        {
          "score": -7,
          "benign_score": 7,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BP6",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "NM_006206.6",
          "gene_symbol": "PDGFRA",
          "hgnc_id": 8803,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "Unknown,AD",
          "hgvs_c": "c.3040G>A",
          "hgvs_p": "p.Ala1014Thr"
        },
        {
          "score": -1,
          "benign_score": 3,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Moderate",
            "BP6"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000507166.5",
          "gene_symbol": "ENSG00000282278",
          "hgnc_id": null,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.2320G>A",
          "hgvs_p": "p.Ala774Thr"
        }
      ],
      "clinvar_disease": " gastrointestinal, multiple and recurrent inflammatory fibroid,Gastrointestinal stromal tumor,Hereditary cancer-predisposing syndrome,Polyps,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:3 LB:1",
      "phenotype_combined": "Gastrointestinal stromal tumor|Hereditary cancer-predisposing syndrome|Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal|not provided",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}