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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: X-72464707-GGCTTGGT-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=72464707&ref=GGCTTGGT&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "X",
      "pos": 72464707,
      "ref": "GGCTTGGT",
      "alt": "G",
      "effect": "frameshift_variant",
      "transcript": "ENST00000373573.9",
      "consequences": [
        {
          "aa_ref": "YQA",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "NM_018486.3",
          "protein_id": "NP_060956.1",
          "transcript_support_level": null,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 377,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 1134,
          "cdna_start": 843,
          "cdna_end": null,
          "cdna_length": 1754,
          "mane_select": "ENST00000373573.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "YQA",
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "ENST00000373573.9",
          "protein_id": "ENSP00000362674.3",
          "transcript_support_level": 1,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 377,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 1134,
          "cdna_start": 843,
          "cdna_end": null,
          "cdna_length": 1754,
          "mane_select": "NM_018486.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "YQA",
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000285547",
          "gene_hgnc_id": null,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "ENST00000648922.1",
          "protein_id": "ENSP00000497072.1",
          "transcript_support_level": null,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 555,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 1670,
          "cdna_start": 843,
          "cdna_end": null,
          "cdna_length": 1752,
          "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": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "n.*453_*459delACCAAGC",
          "hgvs_p": null,
          "transcript": "ENST00000412342.6",
          "protein_id": "ENSP00000400180.1",
          "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": 687,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "n.*453_*459delACCAAGC",
          "hgvs_p": null,
          "transcript": "ENST00000412342.6",
          "protein_id": "ENSP00000400180.1",
          "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": 687,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "YQA",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "ENST00000373568.7",
          "protein_id": "ENSP00000362669.3",
          "transcript_support_level": 5,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 417,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 1254,
          "cdna_start": 842,
          "cdna_end": null,
          "cdna_length": 1625,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "YQA",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "ENST00000648452.1",
          "protein_id": "ENSP00000497268.1",
          "transcript_support_level": null,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 414,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 1245,
          "cdna_start": 865,
          "cdna_end": null,
          "cdna_length": 1865,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "YQA",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "NM_001410725.1",
          "protein_id": "NP_001397654.1",
          "transcript_support_level": null,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 843,
          "cdna_end": null,
          "cdna_length": 1832,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "YQA",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "ENST00000647886.1",
          "protein_id": "ENSP00000497188.1",
          "transcript_support_level": null,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": 859,
          "cdna_end": null,
          "cdna_length": 1807,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "YQA",
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.749_755delACCAAGC",
          "hgvs_p": "p.Tyr250fs",
          "transcript": "ENST00000647980.1",
          "protein_id": "ENSP00000498002.1",
          "transcript_support_level": null,
          "aa_start": 250,
          "aa_end": null,
          "aa_length": 375,
          "cds_start": 749,
          "cds_end": null,
          "cds_length": 1128,
          "cdna_start": 841,
          "cdna_end": null,
          "cdna_length": 1700,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
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        },
        {
          "aa_ref": "YQA",
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          "canonical": false,
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          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "ENST00000647594.1",
          "protein_id": "ENSP00000496814.1",
          "transcript_support_level": null,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 373,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 1122,
          "cdna_start": 865,
          "cdna_end": null,
          "cdna_length": 1785,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
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        },
        {
          "aa_ref": "YQA",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
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          "gene_symbol": "HDAC8",
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          "hgvs_c": "c.755_761delACCAAGC",
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          "protein_id": "ENSP00000497530.1",
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          "cds_start": 755,
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        },
        {
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 7,
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          "intron_rank": null,
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          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.677_683delACCAAGC",
          "hgvs_p": "p.Tyr226fs",
          "transcript": "NM_001410727.1",
          "protein_id": "NP_001397656.1",
          "transcript_support_level": null,
          "aa_start": 226,
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          "aa_length": 351,
          "cds_start": 677,
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          "cdna_start": 765,
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        },
        {
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          "strand": false,
          "consequences": [
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          ],
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          "exon_count": 10,
          "intron_rank": null,
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          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.677_683delACCAAGC",
          "hgvs_p": "p.Tyr226fs",
          "transcript": "ENST00000373583.6",
          "protein_id": "ENSP00000362685.2",
          "transcript_support_level": 5,
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          "aa_end": null,
          "aa_length": 351,
          "cds_start": 677,
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          "cdna_start": 799,
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        },
        {
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          ],
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          "gene_symbol": "HDAC8",
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        },
        {
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          "strand": false,
          "consequences": [
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          ],
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          "exon_count": 10,
          "intron_rank": null,
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          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "ENST00000415409.6",
          "protein_id": "ENSP00000396424.2",
          "transcript_support_level": 5,
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          "cds_start": 755,
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        },
        {
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          "exon_rank_end": null,
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          "intron_rank": null,
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          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs",
          "transcript": "ENST00000648870.1",
          "protein_id": "ENSP00000497599.1",
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          "cds_start": 755,
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          "cdna_start": 856,
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        },
        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.455_461delACCAAGC",
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        },
        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "HDAC8",
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        },
        {
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          "consequences": [
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          ],
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          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HDAC8",
          "gene_hgnc_id": 13315,
          "hgvs_c": "c.482_488delACCAAGC",
          "hgvs_p": "p.Tyr161fs",
          "transcript": "ENST00000647654.1",
          "protein_id": "ENSP00000497568.1",
          "transcript_support_level": null,
          "aa_start": 161,
          "aa_end": null,
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          "cds_start": 482,
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          "cds_length": 939,
          "cdna_start": 570,
          "cdna_end": null,
          "cdna_length": 1516,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "exon_rank_end": null,
          "exon_count": 9,
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      ],
      "gene_symbol": "HDAC8",
      "gene_hgnc_id": 13315,
      "dbsnp": "rs1555993215",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": null,
      "computational_prediction_selected": null,
      "computational_source_selected": null,
      "splice_score_selected": null,
      "splice_prediction_selected": null,
      "splice_source_selected": null,
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": null,
      "bayesdelnoaf_prediction": null,
      "phylop100way_score": 4.739,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": null,
      "spliceai_max_prediction": null,
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
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      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 12,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PVS1,PM2,PP5_Moderate",
      "acmg_by_gene": [
        {
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          "benign_score": 0,
          "pathogenic_score": 12,
          "criteria": [
            "PVS1",
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000373573.9",
          "gene_symbol": "HDAC8",
          "hgnc_id": 13315,
          "effects": [
            "frameshift_variant"
          ],
          "inheritance_mode": "XL,AD",
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs"
        },
        {
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          "benign_score": 0,
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          "criteria": [
            "PVS1",
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000648922.1",
          "gene_symbol": "ENSG00000285547",
          "hgnc_id": null,
          "effects": [
            "frameshift_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.755_761delACCAAGC",
          "hgvs_p": "p.Tyr252fs"
        }
      ],
      "clinvar_disease": "Inborn genetic diseases",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "P:1",
      "phenotype_combined": "Inborn genetic diseases",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}