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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: 10-86912271-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=86912271&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "10",
      "pos": 86912271,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000372037.8",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BMPR1A",
          "gene_hgnc_id": 1076,
          "hgvs_c": "c.562C>T",
          "hgvs_p": "p.Arg188Cys",
          "transcript": "NM_004329.3",
          "protein_id": "NP_004320.2",
          "transcript_support_level": null,
          "aa_start": 188,
          "aa_end": null,
          "aa_length": 532,
          "cds_start": 562,
          "cds_end": null,
          "cds_length": 1599,
          "cdna_start": 1130,
          "cdna_end": null,
          "cdna_length": 6417,
          "mane_select": "ENST00000372037.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BMPR1A",
          "gene_hgnc_id": 1076,
          "hgvs_c": "c.562C>T",
          "hgvs_p": "p.Arg188Cys",
          "transcript": "ENST00000372037.8",
          "protein_id": "ENSP00000361107.2",
          "transcript_support_level": 1,
          "aa_start": 188,
          "aa_end": null,
          "aa_length": 532,
          "cds_start": 562,
          "cds_end": null,
          "cds_length": 1599,
          "cdna_start": 1130,
          "cdna_end": null,
          "cdna_length": 6417,
          "mane_select": "NM_004329.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BMPR1A",
          "gene_hgnc_id": 1076,
          "hgvs_c": "c.637C>T",
          "hgvs_p": "p.Arg213Cys",
          "transcript": "NM_001406559.1",
          "protein_id": "NP_001393488.1",
          "transcript_support_level": null,
          "aa_start": 213,
          "aa_end": null,
          "aa_length": 557,
          "cds_start": 637,
          "cds_end": null,
          "cds_length": 1674,
          "cdna_start": 1205,
          "cdna_end": null,
          "cdna_length": 6492,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BMPR1A",
          "gene_hgnc_id": 1076,
          "hgvs_c": "c.610C>T",
          "hgvs_p": "p.Arg204Cys",
          "transcript": "NM_001406560.1",
          "protein_id": "NP_001393489.1",
          "transcript_support_level": null,
          "aa_start": 204,
          "aa_end": null,
          "aa_length": 548,
          "cds_start": 610,
          "cds_end": null,
          "cds_length": 1647,
          "cdna_start": 1178,
          "cdna_end": null,
          "cdna_length": 6465,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BMPR1A",
          "gene_hgnc_id": 1076,
          "hgvs_c": "c.562C>T",
          "hgvs_p": "p.Arg188Cys",
          "transcript": "NM_001406561.1",
          "protein_id": "NP_001393490.1",
          "transcript_support_level": null,
          "aa_start": 188,
          "aa_end": null,
          "aa_length": 532,
          "cds_start": 562,
          "cds_end": null,
          "cds_length": 1599,
          "cdna_start": 1235,
          "cdna_end": null,
          "cdna_length": 6522,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BMPR1A",
          "gene_hgnc_id": 1076,
          "hgvs_c": "c.562C>T",
          "hgvs_p": "p.Arg188Cys",
          "transcript": "NM_001406562.1",
          "protein_id": "NP_001393491.1",
          "transcript_support_level": null,
          "aa_start": 188,
          "aa_end": null,
          "aa_length": 532,
          "cds_start": 562,
          "cds_end": null,
          "cds_length": 1599,
          "cdna_start": 1276,
          "cdna_end": null,
          "cdna_length": 6563,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BMPR1A",
          "gene_hgnc_id": 1076,
          "hgvs_c": "c.562C>T",
          "hgvs_p": "p.Arg188Cys",
          "transcript": "NM_001406563.1",
          "protein_id": "NP_001393492.1",
          "transcript_support_level": null,
          "aa_start": 188,
          "aa_end": null,
          "aa_length": 532,
          "cds_start": 562,
          "cds_end": null,
          "cds_length": 1599,
          "cdna_start": 1527,
          "cdna_end": null,
          "cdna_length": 6814,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BMPR1A",
          "gene_hgnc_id": 1076,
          "hgvs_c": "c.562C>T",
          "hgvs_p": "p.Arg188Cys",
          "transcript": "NM_001406564.1",
          "protein_id": "NP_001393493.1",
          "transcript_support_level": null,
          "aa_start": 188,
          "aa_end": null,
          "aa_length": 532,
          "cds_start": 562,
          "cds_end": null,
          "cds_length": 1599,
          "cdna_start": 1135,
          "cdna_end": null,
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          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "R",
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 10,
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          "gene_symbol": "BMPR1A",
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          "hgvs_c": "c.562C>T",
          "hgvs_p": "p.Arg188Cys",
          "transcript": "NM_001406565.1",
          "protein_id": "NP_001393494.1",
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          "cdna_start": 1390,
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        {
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          "intron_rank": null,
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          "gene_symbol": "BMPR1A",
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          "hgvs_c": "c.562C>T",
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          "transcript": "NM_001406566.1",
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        {
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      ],
      "gene_symbol": "BMPR1A",
      "gene_hgnc_id": 1076,
      "dbsnp": "rs879254272",
      "frequency_reference_population": 0.000014253701,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 23,
      "gnomad_exomes_af": 0.0000150526,
      "gnomad_genomes_af": 0.00000657566,
      "gnomad_exomes_ac": 22,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.26316845417022705,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.212,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0863,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.26,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 1.929,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.02,
      "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": "ENST00000372037.8",
          "gene_symbol": "BMPR1A",
          "hgnc_id": 1076,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,Unknown",
          "hgvs_c": "c.562C>T",
          "hgvs_p": "p.Arg188Cys"
        }
      ],
      "clinvar_disease": " 2, hereditary mixed,BMPR1A-related disorder,Hereditary cancer-predisposing syndrome,Juvenile polyposis syndrome,Polyposis syndrome,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:7 LB:3",
      "phenotype_combined": "not provided|Hereditary cancer-predisposing syndrome|not specified|Juvenile polyposis syndrome|BMPR1A-related disorder|Polyposis syndrome, hereditary mixed, 2|Polyposis syndrome, hereditary mixed, 2;Juvenile polyposis syndrome",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}