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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: 3-129483544-G-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=129483544&ref=G&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 129483544,
      "ref": "G",
      "alt": "T",
      "effect": "synonymous_variant",
      "transcript": "ENST00000348417.7",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser",
          "transcript": "NM_052989.3",
          "protein_id": "NP_443715.1",
          "transcript_support_level": null,
          "aa_start": 571,
          "aa_end": null,
          "aa_length": 1241,
          "cds_start": 1713,
          "cds_end": null,
          "cds_length": 3726,
          "cdna_start": 1820,
          "cdna_end": null,
          "cdna_length": 4075,
          "mane_select": "ENST00000348417.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser",
          "transcript": "ENST00000348417.7",
          "protein_id": "ENSP00000324005.4",
          "transcript_support_level": 1,
          "aa_start": 571,
          "aa_end": null,
          "aa_length": 1241,
          "cds_start": 1713,
          "cds_end": null,
          "cds_length": 3726,
          "cdna_start": 1820,
          "cdna_end": null,
          "cdna_length": 4075,
          "mane_select": "NM_052989.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1866G>T",
          "hgvs_p": "p.Ser622Ser",
          "transcript": "ENST00000296266.7",
          "protein_id": "ENSP00000296266.3",
          "transcript_support_level": 1,
          "aa_start": 622,
          "aa_end": null,
          "aa_length": 1292,
          "cds_start": 1866,
          "cds_end": null,
          "cds_length": 3879,
          "cdna_start": 2058,
          "cdna_end": null,
          "cdna_length": 4151,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1689G>T",
          "hgvs_p": "p.Ser563Ser",
          "transcript": "ENST00000507564.5",
          "protein_id": "ENSP00000425536.1",
          "transcript_support_level": 1,
          "aa_start": 563,
          "aa_end": null,
          "aa_length": 1234,
          "cds_start": 1689,
          "cds_end": null,
          "cds_length": 3705,
          "cdna_start": 1808,
          "cdna_end": null,
          "cdna_length": 3824,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1536G>T",
          "hgvs_p": "p.Ser512Ser",
          "transcript": "ENST00000347300.6",
          "protein_id": "ENSP00000323973.3",
          "transcript_support_level": 1,
          "aa_start": 512,
          "aa_end": null,
          "aa_length": 1182,
          "cds_start": 1536,
          "cds_end": null,
          "cds_length": 3549,
          "cdna_start": 1742,
          "cdna_end": null,
          "cdna_length": 3841,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1380G>T",
          "hgvs_p": "p.Ser460Ser",
          "transcript": "ENST00000349441.6",
          "protein_id": "ENSP00000324165.3",
          "transcript_support_level": 1,
          "aa_start": 460,
          "aa_end": null,
          "aa_length": 1131,
          "cds_start": 1380,
          "cds_end": null,
          "cds_length": 3396,
          "cdna_start": 1467,
          "cdna_end": null,
          "cdna_length": 3569,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1866G>T",
          "hgvs_p": "p.Ser622Ser",
          "transcript": "NM_052985.4",
          "protein_id": "NP_443711.2",
          "transcript_support_level": null,
          "aa_start": 622,
          "aa_end": null,
          "aa_length": 1292,
          "cds_start": 1866,
          "cds_end": null,
          "cds_length": 3879,
          "cdna_start": 1973,
          "cdna_end": null,
          "cdna_length": 4228,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser",
          "transcript": "ENST00000689643.1",
          "protein_id": "ENSP00000509801.1",
          "transcript_support_level": null,
          "aa_start": 571,
          "aa_end": null,
          "aa_length": 1265,
          "cds_start": 1713,
          "cds_end": null,
          "cds_length": 3798,
          "cdna_start": 1917,
          "cdna_end": null,
          "cdna_length": 4030,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser",
          "transcript": "NM_001410808.1",
          "protein_id": "NP_001397737.1",
          "transcript_support_level": null,
          "aa_start": 571,
          "aa_end": null,
          "aa_length": 1242,
          "cds_start": 1713,
          "cds_end": null,
          "cds_length": 3729,
          "cdna_start": 1820,
          "cdna_end": null,
          "cdna_length": 4078,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser",
          "transcript": "ENST00000692242.1",
          "protein_id": "ENSP00000509878.1",
          "transcript_support_level": null,
          "aa_start": 571,
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          "aa_length": 1242,
          "cds_start": 1713,
          "cds_end": null,
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          "cdna_start": 1917,
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          "cdna_length": 4178,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
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          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1689G>T",
          "hgvs_p": "p.Ser563Ser",
          "transcript": "NM_001280541.2",
          "protein_id": "NP_001267470.1",
          "transcript_support_level": null,
          "aa_start": 563,
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          "cds_start": 1689,
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          "cds_length": 3705,
          "cdna_start": 1796,
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          "cdna_length": 4054,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
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          "intron_rank": null,
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          "gene_symbol": "IFT122",
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          "hgvs_c": "c.1689G>T",
          "hgvs_p": "p.Ser563Ser",
          "transcript": "ENST00000689313.1",
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        {
          "aa_ref": "S",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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          "gene_symbol": "IFT122",
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          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser",
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          "protein_id": "ENSP00000509225.1",
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        {
          "aa_ref": "S",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 15,
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          "intron_rank": null,
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          "gene_symbol": "IFT122",
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          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser",
          "transcript": "NM_001410809.1",
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        {
          "aa_ref": "S",
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        {
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          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser",
          "transcript": "ENST00000693489.1",
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        },
        {
          "aa_ref": "S",
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          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1536G>T",
          "hgvs_p": "p.Ser512Ser",
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        {
          "aa_ref": "S",
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          "gene_symbol": "IFT122",
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          "hgvs_c": "c.1557G>T",
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        },
        {
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        },
        {
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          "strand": true,
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          "gene_symbol": "IFT122",
          "gene_hgnc_id": 13556,
          "hgvs_c": "c.1557G>T",
          "hgvs_p": "p.Ser519Ser",
          "transcript": "NM_001438638.1",
          "protein_id": "NP_001425567.1",
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          "cdna_length": 3919,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
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          "intron_rank": null,
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          "gene_symbol": "IFT122",
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      "dbsnp": "rs150174636",
      "frequency_reference_population": 0.011060486,
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      "allele_count_reference_population": 17852,
      "gnomad_exomes_af": 0.0110674,
      "gnomad_genomes_af": 0.010994,
      "gnomad_exomes_ac": 16179,
      "gnomad_genomes_ac": 1673,
      "gnomad_exomes_homalt": 152,
      "gnomad_genomes_homalt": 12,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.699999988079071,
      "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": -0.7,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -2.412,
      "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,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": "ENST00000348417.7",
          "gene_symbol": "IFT122",
          "hgnc_id": 13556,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1713G>T",
          "hgvs_p": "p.Ser571Ser"
        },
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000765520.1",
          "gene_symbol": "ENSG00000299667",
          "hgnc_id": null,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.406C>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Connective tissue disorder,Cranioectodermal dysplasia,Cranioectodermal dysplasia 1,not provided",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2 B:3",
      "phenotype_combined": "Cranioectodermal dysplasia|Cranioectodermal dysplasia 1|not provided|Connective tissue disorder",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}