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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: 4-55443770-T-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=55443770&ref=T&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 55443770,
      "ref": "T",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_004898.4",
      "consequences": [
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "NM_004898.4",
          "protein_id": "NP_004889.1",
          "transcript_support_level": null,
          "aa_start": 607,
          "aa_end": null,
          "aa_length": 846,
          "cds_start": 1819,
          "cds_end": null,
          "cds_length": 2541,
          "cdna_start": 2236,
          "cdna_end": null,
          "cdna_length": 10470,
          "mane_select": "ENST00000513440.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "ENST00000513440.6",
          "protein_id": "ENSP00000426983.1",
          "transcript_support_level": 1,
          "aa_start": 607,
          "aa_end": null,
          "aa_length": 846,
          "cds_start": 1819,
          "cds_end": null,
          "cds_length": 2541,
          "cdna_start": 2236,
          "cdna_end": null,
          "cdna_length": 10470,
          "mane_select": "NM_004898.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "ENST00000309964.8",
          "protein_id": "ENSP00000308741.4",
          "transcript_support_level": 1,
          "aa_start": 607,
          "aa_end": null,
          "aa_length": 846,
          "cds_start": 1819,
          "cds_end": null,
          "cds_length": 2541,
          "cdna_start": 2070,
          "cdna_end": null,
          "cdna_length": 10304,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "ENST00000381322.5",
          "protein_id": "ENSP00000370723.1",
          "transcript_support_level": 1,
          "aa_start": 607,
          "aa_end": null,
          "aa_length": 846,
          "cds_start": 1819,
          "cds_end": null,
          "cds_length": 2541,
          "cdna_start": 2745,
          "cdna_end": null,
          "cdna_length": 4059,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "n.401A>T",
          "hgvs_p": null,
          "transcript": "ENST00000511124.1",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3932,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "NM_001267843.2",
          "protein_id": "NP_001254772.1",
          "transcript_support_level": null,
          "aa_start": 607,
          "aa_end": null,
          "aa_length": 846,
          "cds_start": 1819,
          "cds_end": null,
          "cds_length": 2541,
          "cdna_start": 2745,
          "cdna_end": null,
          "cdna_length": 10979,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "XM_005265787.3",
          "protein_id": "XP_005265844.1",
          "transcript_support_level": null,
          "aa_start": 607,
          "aa_end": null,
          "aa_length": 846,
          "cds_start": 1819,
          "cds_end": null,
          "cds_length": 2541,
          "cdna_start": 2243,
          "cdna_end": null,
          "cdna_length": 10477,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "XM_011534410.3",
          "protein_id": "XP_011532712.1",
          "transcript_support_level": null,
          "aa_start": 607,
          "aa_end": null,
          "aa_length": 846,
          "cds_start": 1819,
          "cds_end": null,
          "cds_length": 2541,
          "cdna_start": 2082,
          "cdna_end": null,
          "cdna_length": 10316,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "XM_011534411.3",
          "protein_id": "XP_011532713.1",
          "transcript_support_level": null,
          "aa_start": 607,
          "aa_end": null,
          "aa_length": 846,
          "cds_start": 1819,
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          "cdna_start": 2089,
          "cdna_end": null,
          "cdna_length": 10323,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "I",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
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          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "XM_017008854.2",
          "protein_id": "XP_016864343.1",
          "transcript_support_level": null,
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          "cds_start": 1819,
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          "cdna_start": 2393,
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          "mane_select": null,
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        {
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          "hgvs_c": "c.1819A>T",
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          "transcript": "XM_024454284.2",
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        {
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          "consequences": [
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          "exon_rank": 21,
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          "intron_rank": null,
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        {
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          "gene_symbol": "CLOCK",
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          "transcript": "XM_047416433.1",
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        {
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          "gene_symbol": "CLOCK",
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        {
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        {
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          "gene_symbol": "CLOCK",
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          "hgvs_c": "c.1819A>T",
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          "transcript": "XM_047416439.1",
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        },
        {
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          ],
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          "intron_rank": null,
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          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe",
          "transcript": "XM_047416440.1",
          "protein_id": "XP_047272396.1",
          "transcript_support_level": null,
          "aa_start": 607,
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          "aa_length": 846,
          "cds_start": 1819,
          "cds_end": null,
          "cds_length": 2541,
          "cdna_start": 2043,
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          "cdna_length": 10277,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
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          "transcript": "ENST00000608091.1",
          "protein_id": "ENSP00000476531.1",
          "transcript_support_level": 3,
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          "cds_start": -4,
          "cds_end": null,
          "cds_length": 474,
          "cdna_start": null,
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          "cdna_length": 1567,
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          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 3,
          "intron_rank": 2,
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          "gene_symbol": "TMEM165",
          "gene_hgnc_id": 30760,
          "hgvs_c": "n.*271-8469T>A",
          "hgvs_p": null,
          "transcript": "ENST00000506103.2",
          "protein_id": "ENSP00000476621.1",
          "transcript_support_level": 3,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 572,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 6,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "TMEM165",
          "gene_hgnc_id": 30760,
          "hgvs_c": "c.899-8469T>A",
          "hgvs_p": null,
          "transcript": "XM_011534394.4",
          "protein_id": "XP_011532696.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 321,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 966,
          "cdna_start": null,
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          "cdna_length": 2290,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
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          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CLOCK",
          "gene_hgnc_id": 2082,
          "hgvs_c": "n.-15A>T",
          "hgvs_p": null,
          "transcript": "ENST00000479384.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 426,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "CLOCK",
      "gene_hgnc_id": 2082,
      "dbsnp": "rs141058115",
      "frequency_reference_population": 0.00002540238,
      "hom_count_reference_population": 1,
      "allele_count_reference_population": 41,
      "gnomad_exomes_af": 0.0000273633,
      "gnomad_genomes_af": 0.00000656987,
      "gnomad_exomes_ac": 40,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 1,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.03845062851905823,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.018,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0752,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.59,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.245,
      "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": -8,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BS2",
      "acmg_by_gene": [
        {
          "score": -8,
          "benign_score": 8,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "NM_004898.4",
          "gene_symbol": "CLOCK",
          "hgnc_id": 2082,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.1819A>T",
          "hgvs_p": "p.Ile607Phe"
        },
        {
          "score": -4,
          "benign_score": 4,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000608091.1",
          "gene_symbol": "TMEM165",
          "hgnc_id": 30760,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.407-8469T>A",
          "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
}