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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: 22-33283252-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=33283252&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "22",
      "pos": 33283252,
      "ref": "T",
      "alt": "C",
      "effect": "synonymous_variant",
      "transcript": "ENST00000397394.8",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "NM_133642.5",
          "protein_id": "NP_598397.1",
          "transcript_support_level": null,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 2391,
          "cdna_end": null,
          "cdna_length": 4753,
          "mane_select": "ENST00000397394.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "ENST00000397394.8",
          "protein_id": "ENSP00000380549.2",
          "transcript_support_level": 5,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 2391,
          "cdna_end": null,
          "cdna_length": 4753,
          "mane_select": "NM_133642.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "ENST00000354992.7",
          "protein_id": "ENSP00000347088.2",
          "transcript_support_level": 1,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 2399,
          "cdna_end": null,
          "cdna_length": 4193,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1671A>G",
          "hgvs_p": "p.Ser557Ser",
          "transcript": "ENST00000402320.6",
          "protein_id": "ENSP00000385223.1",
          "transcript_support_level": 1,
          "aa_start": 557,
          "aa_end": null,
          "aa_length": 704,
          "cds_start": 1671,
          "cds_end": null,
          "cds_length": 2115,
          "cdna_start": 2173,
          "cdna_end": null,
          "cdna_length": 3967,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "NM_001362949.2",
          "protein_id": "NP_001349878.1",
          "transcript_support_level": null,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 2176,
          "cdna_end": null,
          "cdna_length": 4538,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "NM_001362951.2",
          "protein_id": "NP_001349880.1",
          "transcript_support_level": null,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 1996,
          "cdna_end": null,
          "cdna_length": 4358,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "NM_001362953.2",
          "protein_id": "NP_001349882.1",
          "transcript_support_level": null,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 2113,
          "cdna_end": null,
          "cdna_length": 4475,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "NM_001378624.1",
          "protein_id": "NP_001365553.1",
          "transcript_support_level": null,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 2059,
          "cdna_end": null,
          "cdna_length": 4421,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "NM_001378625.1",
          "protein_id": "NP_001365554.1",
          "transcript_support_level": null,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 2194,
          "cdna_end": null,
          "cdna_length": 4556,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "NM_001378626.1",
          "protein_id": "NP_001365555.1",
          "transcript_support_level": null,
          "aa_start": 609,
          "aa_end": null,
          "aa_length": 756,
          "cds_start": 1827,
          "cds_end": null,
          "cds_length": 2271,
          "cdna_start": 2131,
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          "cdna_length": 4493,
          "mane_select": null,
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          "biotype": null,
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        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 14,
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          "intron_rank": null,
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          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "NM_004737.7",
          "protein_id": "NP_004728.1",
          "transcript_support_level": null,
          "aa_start": 609,
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          "aa_length": 756,
          "cds_start": 1827,
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          "cds_length": 2271,
          "cdna_start": 2454,
          "cdna_end": null,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
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          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "LARGE1",
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          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "ENST00000413114.6",
          "protein_id": "ENSP00000415546.2",
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          "cds_start": 1827,
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        {
          "aa_ref": "S",
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          "canonical": false,
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          "strand": false,
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          "hgvs_c": "c.1827A>G",
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          "transcript": "ENST00000675416.1",
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        {
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "ENST00000676070.1",
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        },
        {
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        {
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          "strand": false,
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          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser",
          "transcript": "ENST00000676370.1",
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        {
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          "strand": false,
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          "exon_rank": 11,
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          "exon_count": 13,
          "intron_rank": null,
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          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1701A>G",
          "hgvs_p": "p.Ser567Ser",
          "transcript": "ENST00000674668.1",
          "protein_id": "ENSP00000502103.1",
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        },
        {
          "aa_ref": "S",
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          "intron_rank": null,
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          "gene_symbol": "LARGE1",
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        },
        {
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        },
        {
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          "intron_rank": null,
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          "gene_symbol": "LARGE1",
          "gene_hgnc_id": 6511,
          "hgvs_c": "c.1623A>G",
          "hgvs_p": "p.Ser541Ser",
          "transcript": "ENST00000675277.1",
          "protein_id": "ENSP00000502702.1",
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          "cdna_length": 2355,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
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          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
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      ],
      "gene_symbol": "LARGE1",
      "gene_hgnc_id": 6511,
      "dbsnp": "rs11913417",
      "frequency_reference_population": 0.009761356,
      "hom_count_reference_population": 386,
      "allele_count_reference_population": 15756,
      "gnomad_exomes_af": 0.00845278,
      "gnomad_genomes_af": 0.0223275,
      "gnomad_exomes_ac": 12357,
      "gnomad_genomes_ac": 3399,
      "gnomad_exomes_homalt": 296,
      "gnomad_genomes_homalt": 90,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.9200000166893005,
      "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": -0.92,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -1.836,
      "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": -21,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
      "acmg_by_gene": [
        {
          "score": -21,
          "benign_score": 21,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000397394.8",
          "gene_symbol": "LARGE1",
          "hgnc_id": 6511,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1827A>G",
          "hgvs_p": "p.Ser609Ser"
        }
      ],
      "clinvar_disease": " type A6,Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies),Muscular dystrophy-dystroglycanopathy type B6,not provided,not specified",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "B:7",
      "phenotype_combined": "not specified|Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A6|Muscular dystrophy-dystroglycanopathy type B6|not provided",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}