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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: 1-117957091-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=117957091&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 117957091,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_006784.3",
      "consequences": [
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala",
          "transcript": "NM_006784.3",
          "protein_id": "NP_006775.1",
          "transcript_support_level": null,
          "aa_start": 826,
          "aa_end": null,
          "aa_length": 943,
          "cds_start": 2477,
          "cds_end": null,
          "cds_length": 2832,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000349139.6",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_006784.3"
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala",
          "transcript": "ENST00000349139.6",
          "protein_id": "ENSP00000308179.4",
          "transcript_support_level": 1,
          "aa_start": 826,
          "aa_end": null,
          "aa_length": 943,
          "cds_start": 2477,
          "cds_end": null,
          "cds_length": 2832,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_006784.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000349139.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 49,
          "intron_rank": 48,
          "intron_rank_end": null,
          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "c.*1-3042A>G",
          "hgvs_p": null,
          "transcript": "NM_206996.4",
          "protein_id": "NP_996879.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 2223,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 6672,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000336338.10",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_206996.4"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 49,
          "intron_rank": 48,
          "intron_rank_end": null,
          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "c.*1-3042A>G",
          "hgvs_p": null,
          "transcript": "ENST00000336338.10",
          "protein_id": "ENSP00000337804.5",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 2223,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 6672,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_206996.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000336338.10"
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala",
          "transcript": "ENST00000880604.1",
          "protein_id": "ENSP00000550663.1",
          "transcript_support_level": null,
          "aa_start": 826,
          "aa_end": null,
          "aa_length": 943,
          "cds_start": 2477,
          "cds_end": null,
          "cds_length": 2832,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000880604.1"
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala",
          "transcript": "ENST00000880605.1",
          "protein_id": "ENSP00000550664.1",
          "transcript_support_level": null,
          "aa_start": 826,
          "aa_end": null,
          "aa_length": 943,
          "cds_start": 2477,
          "cds_end": null,
          "cds_length": 2832,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000880605.1"
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 26,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala",
          "transcript": "ENST00000928994.1",
          "protein_id": "ENSP00000599053.1",
          "transcript_support_level": null,
          "aa_start": 826,
          "aa_end": null,
          "aa_length": 943,
          "cds_start": 2477,
          "cds_end": null,
          "cds_length": 2832,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000928994.1"
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 26,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala",
          "transcript": "ENST00000947751.1",
          "protein_id": "ENSP00000617810.1",
          "transcript_support_level": null,
          "aa_start": 826,
          "aa_end": null,
          "aa_length": 943,
          "cds_start": 2477,
          "cds_end": null,
          "cds_length": 2832,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000947751.1"
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 26,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala",
          "transcript": "ENST00000947753.1",
          "protein_id": "ENSP00000617812.1",
          "transcript_support_level": null,
          "aa_start": 826,
          "aa_end": null,
          "aa_length": 943,
          "cds_start": 2477,
          "cds_end": null,
          "cds_length": 2832,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000947753.1"
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala",
          "transcript": "ENST00000947754.1",
          "protein_id": "ENSP00000617813.1",
          "transcript_support_level": null,
          "aa_start": 826,
          "aa_end": null,
          "aa_length": 943,
          "cds_start": 2477,
          "cds_end": null,
          "cds_length": 2832,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000947754.1"
        },
        {
          "aa_ref": "V",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "WDR3",
          "gene_hgnc_id": 12755,
          "hgvs_c": "c.2420T>C",
          "hgvs_p": "p.Val807Ala",
          "transcript": "ENST00000947752.1",
          "protein_id": "ENSP00000617811.1",
          "transcript_support_level": null,
          "aa_start": 807,
          "aa_end": null,
          "aa_length": 924,
          "cds_start": 2420,
          "cds_end": null,
          "cds_length": 2775,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000947752.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 48,
          "intron_rank": 47,
          "intron_rank_end": null,
          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "c.*1-3042A>G",
          "hgvs_p": null,
          "transcript": "XM_006710426.4",
          "protein_id": "XP_006710489.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 2185,
          "cds_start": null,
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          "cds_length": 6558,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 48,
          "intron_rank": 47,
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          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "c.*1-3042A>G",
          "hgvs_p": null,
          "transcript": "XM_011540934.2",
          "protein_id": "XP_011539236.1",
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          "cds_start": null,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_011540934.2"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 48,
          "intron_rank": 47,
          "intron_rank_end": null,
          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "c.*1-3042A>G",
          "hgvs_p": null,
          "transcript": "XM_006710427.4",
          "protein_id": "XP_006710490.1",
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          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "c.*1-3042A>G",
          "hgvs_p": null,
          "transcript": "XM_011540935.3",
          "protein_id": "XP_011539237.1",
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          "cdna_start": null,
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          "biotype": "protein_coding",
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 41,
          "intron_rank": 40,
          "intron_rank_end": null,
          "gene_symbol": "SPAG17",
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          "hgvs_c": "c.*1-3042A>G",
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          "transcript": "XM_011540936.3",
          "protein_id": "XP_011539238.1",
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          "cds_start": null,
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        {
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          "canonical": false,
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          "exon_count": 40,
          "intron_rank": 39,
          "intron_rank_end": null,
          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "c.*1-3042A>G",
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          "transcript": "XM_011540937.3",
          "protein_id": "XP_011539239.1",
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        {
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          "gene_symbol": "SPAG17",
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          "hgvs_c": "c.*1-3042A>G",
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          "gene_symbol": "SPAG17",
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          "hgvs_c": "c.*1-3042A>G",
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          "biotype": "protein_coding",
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        },
        {
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          "strand": false,
          "consequences": [
            "intron_variant"
          ],
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          "exon_count": 37,
          "intron_rank": 36,
          "intron_rank_end": null,
          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "c.*1-3042A>G",
          "hgvs_p": null,
          "transcript": "XM_011540939.3",
          "protein_id": "XP_011539241.1",
          "transcript_support_level": null,
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          "biotype": "protein_coding",
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        },
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        {
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          "gene_symbol": "SPAG17",
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        },
        {
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            "intron_variant"
          ],
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          "gene_symbol": "SPAG17",
          "gene_hgnc_id": 26620,
          "hgvs_c": "n.6744-1861A>G",
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          "transcript": "XR_946574.2",
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          "aa_length": null,
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          "biotype": "pseudogene",
          "feature": "XR_946574.2"
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      ],
      "gene_symbol": "WDR3",
      "gene_hgnc_id": 12755,
      "dbsnp": "rs369554244",
      "frequency_reference_population": 0.00000561647,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 9,
      "gnomad_exomes_af": 0.0000020687,
      "gnomad_genomes_af": 0.0000394099,
      "gnomad_exomes_ac": 3,
      "gnomad_genomes_ac": 6,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.7651534080505371,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.544,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.6121,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.03,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 7.921,
      "phylop100way_prediction": "Pathogenic",
      "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": 3,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP3",
      "acmg_by_gene": [
        {
          "score": 3,
          "benign_score": 0,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_006784.3",
          "gene_symbol": "WDR3",
          "hgnc_id": 12755,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.2477T>C",
          "hgvs_p": "p.Val826Ala"
        },
        {
          "score": 3,
          "benign_score": 0,
          "pathogenic_score": 3,
          "criteria": [
            "PM2",
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_206996.4",
          "gene_symbol": "SPAG17",
          "hgnc_id": 26620,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR,Unknown",
          "hgvs_c": "c.*1-3042A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}