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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: 12-101661240-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=101661240&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "12",
      "pos": 101661240,
      "ref": "C",
      "alt": "T",
      "effect": "synonymous_variant",
      "transcript": "ENST00000361466.7",
      "consequences": [
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.2010C>T",
          "hgvs_p": "p.Tyr670Tyr",
          "transcript": "NM_002465.4",
          "protein_id": "NP_002456.2",
          "transcript_support_level": null,
          "aa_start": 670,
          "aa_end": null,
          "aa_length": 1171,
          "cds_start": 2010,
          "cds_end": null,
          "cds_length": 3516,
          "cdna_start": 2110,
          "cdna_end": null,
          "cdna_length": 4082,
          "mane_select": "ENST00000361466.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.2010C>T",
          "hgvs_p": "p.Tyr670Tyr",
          "transcript": "ENST00000361466.7",
          "protein_id": "ENSP00000354849.2",
          "transcript_support_level": 1,
          "aa_start": 670,
          "aa_end": null,
          "aa_length": 1171,
          "cds_start": 2010,
          "cds_end": null,
          "cds_length": 3516,
          "cdna_start": 2110,
          "cdna_end": null,
          "cdna_length": 4082,
          "mane_select": "NM_002465.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.2010C>T",
          "hgvs_p": "p.Tyr670Tyr",
          "transcript": "ENST00000361685.6",
          "protein_id": "ENSP00000354845.2",
          "transcript_support_level": 1,
          "aa_start": 670,
          "aa_end": null,
          "aa_length": 1148,
          "cds_start": 2010,
          "cds_end": null,
          "cds_length": 3447,
          "cdna_start": 2110,
          "cdna_end": null,
          "cdna_length": 3871,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.1935C>T",
          "hgvs_p": "p.Tyr645Tyr",
          "transcript": "ENST00000545503.6",
          "protein_id": "ENSP00000440034.2",
          "transcript_support_level": 1,
          "aa_start": 645,
          "aa_end": null,
          "aa_length": 1146,
          "cds_start": 1935,
          "cds_end": null,
          "cds_length": 3441,
          "cdna_start": 2010,
          "cdna_end": null,
          "cdna_length": 3569,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.1899C>T",
          "hgvs_p": "p.Tyr633Tyr",
          "transcript": "ENST00000541119.5",
          "protein_id": "ENSP00000442847.1",
          "transcript_support_level": 1,
          "aa_start": 633,
          "aa_end": null,
          "aa_length": 1134,
          "cds_start": 1899,
          "cds_end": null,
          "cds_length": 3405,
          "cdna_start": 1974,
          "cdna_end": null,
          "cdna_length": 3533,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.1878C>T",
          "hgvs_p": "p.Tyr626Tyr",
          "transcript": "ENST00000536007.5",
          "protein_id": "ENSP00000446128.1",
          "transcript_support_level": 1,
          "aa_start": 626,
          "aa_end": null,
          "aa_length": 1127,
          "cds_start": 1878,
          "cds_end": null,
          "cds_length": 3384,
          "cdna_start": 1953,
          "cdna_end": null,
          "cdna_length": 3512,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.1935C>T",
          "hgvs_p": "p.Tyr645Tyr",
          "transcript": "ENST00000553190.5",
          "protein_id": "ENSP00000447900.1",
          "transcript_support_level": 1,
          "aa_start": 645,
          "aa_end": null,
          "aa_length": 1123,
          "cds_start": 1935,
          "cds_end": null,
          "cds_length": 3372,
          "cdna_start": 2022,
          "cdna_end": null,
          "cdna_length": 3777,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.1857C>T",
          "hgvs_p": "p.Tyr619Tyr",
          "transcript": "ENST00000547405.5",
          "protein_id": "ENSP00000448175.1",
          "transcript_support_level": 1,
          "aa_start": 619,
          "aa_end": null,
          "aa_length": 1120,
          "cds_start": 1857,
          "cds_end": null,
          "cds_length": 3363,
          "cdna_start": 2079,
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          "cdna_length": 3834,
          "mane_select": null,
          "mane_plus": null,
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          "feature": null
        },
        {
          "aa_ref": "Y",
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          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
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          "intron_rank": null,
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          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.1638C>T",
          "hgvs_p": "p.Tyr546Tyr",
          "transcript": "ENST00000551300.5",
          "protein_id": "ENSP00000447116.1",
          "transcript_support_level": 1,
          "aa_start": 546,
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          "cds_start": 1638,
          "cds_end": null,
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          "mane_select": null,
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        },
        {
          "aa_ref": "Y",
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 20,
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          "intron_rank": null,
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          "gene_symbol": "MYBPC1",
          "gene_hgnc_id": 7549,
          "hgvs_c": "c.2010C>T",
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          "transcript": "NM_001404675.1",
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        {
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          "gene_symbol": "MYBPC1",
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        {
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          "gene_symbol": "MYBPC1",
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          "hgvs_c": "c.1899C>T",
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        {
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          ],
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          "exon_count": 4,
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          "gene_symbol": "ENSG00000257514",
          "gene_hgnc_id": null,
          "hgvs_c": "n.72-845G>A",
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          "transcript": "ENST00000774501.1",
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        },
        {
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          ],
          "exon_rank": null,
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          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "LOC124902996",
          "gene_hgnc_id": null,
          "hgvs_c": "n.85-845G>A",
          "hgvs_p": null,
          "transcript": "XR_007063422.1",
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          "aa_length": null,
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        },
        {
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          "exon_count": 3,
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          "gene_symbol": "LOC124902996",
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          "hgvs_c": "n.85-832G>A",
          "hgvs_p": null,
          "transcript": "XR_007063423.1",
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          "cdna_length": 327,
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        }
      ],
      "gene_symbol": "MYBPC1",
      "gene_hgnc_id": 7549,
      "dbsnp": "rs77045393",
      "frequency_reference_population": 0.0015334189,
      "hom_count_reference_population": 29,
      "allele_count_reference_population": 2472,
      "gnomad_exomes_af": 0.000910389,
      "gnomad_genomes_af": 0.0075065,
      "gnomad_exomes_ac": 1329,
      "gnomad_genomes_ac": 1143,
      "gnomad_exomes_homalt": 18,
      "gnomad_genomes_homalt": 11,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.6100000143051147,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.61,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.262,
      "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": -21,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -21,
          "benign_score": 21,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000361466.7",
          "gene_symbol": "MYBPC1",
          "hgnc_id": 7549,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.2010C>T",
          "hgvs_p": "p.Tyr670Tyr"
        },
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000774501.1",
          "gene_symbol": "ENSG00000257514",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.72-845G>A",
          "hgvs_p": null
        },
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "XR_007063422.1",
          "gene_symbol": "LOC124902996",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.85-845G>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " distal, type 1B,Arthrogryposis,not provided,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2 B:5",
      "phenotype_combined": "not specified|not provided|Arthrogryposis, distal, type 1B",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}