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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-10495692-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=10495692&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "X",
      "pos": 10495692,
      "ref": "C",
      "alt": "T",
      "effect": "splice_acceptor_variant,intron_variant",
      "transcript": "ENST00000317552.9",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "NM_000381.4",
          "protein_id": "NP_000372.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6168,
          "mane_select": "ENST00000317552.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "ENST00000317552.9",
          "protein_id": "ENSP00000312678.4",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6168,
          "mane_select": "NM_000381.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "ENST00000380779.5",
          "protein_id": "ENSP00000370156.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6044,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "ENST00000380780.5",
          "protein_id": "ENSP00000370157.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6195,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "ENST00000380787.5",
          "protein_id": "ENSP00000370164.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5973,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "ENST00000380782.6",
          "protein_id": "ENSP00000370159.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 552,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 1659,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3352,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.910-1G>A",
          "hgvs_p": null,
          "transcript": "ENST00000616003.5",
          "protein_id": "ENSP00000484712.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 540,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 1623,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1927,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.910-1G>A",
          "hgvs_p": null,
          "transcript": "ENST00000675073.1",
          "protein_id": "ENSP00000501707.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 718,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2157,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2369,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "NM_001098624.2",
          "protein_id": "NP_001092094.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2004,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6393,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "NM_001193277.1",
          "protein_id": "NP_001180206.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": -4,
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          "cds_length": 2004,
          "cdna_start": null,
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          "cdna_length": 6252,
          "mane_select": null,
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          "biotype": null,
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_acceptor_variant",
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          ],
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          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "NM_001347733.2",
          "protein_id": "NP_001334662.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 667,
          "cds_start": -4,
          "cds_end": null,
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          "cdna_start": null,
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          "cdna_length": 6492,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
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          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
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          "aa_length": 667,
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        {
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          ],
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          "exon_count": 11,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
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          "transcript": "ENST00000380785.5",
          "protein_id": "ENSP00000370162.1",
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          "cds_start": -4,
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        },
        {
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          "canonical": false,
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          "consequences": [
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            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 10,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null,
          "transcript": "ENST00000413894.6",
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        {
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          "gene_symbol": "MID1",
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        {
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          "consequences": [
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          "exon_count": 9,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.757-13064G>A",
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          "transcript": "ENST00000691943.1",
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        {
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          "intron_rank": 3,
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          "gene_symbol": "MID1",
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          "hgvs_c": "c.643-1G>A",
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          "transcript": "NM_033289.2",
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          "gene_symbol": "MID1",
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          ],
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          "intron_rank": 3,
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          "gene_symbol": "MID1",
          "gene_hgnc_id": 7095,
          "hgvs_c": "c.910-1G>A",
          "hgvs_p": null,
          "transcript": "NM_001193278.1",
          "protein_id": "NP_001180207.1",
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          "cdna_start": null,
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        },
        {
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          ],
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        {
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          "gene_symbol": "MID1",
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          "hgvs_c": "c.-111-1G>A",
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          "transcript": "ENST00000674917.1",
          "protein_id": "ENSP00000502171.1",
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        {
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          "gene_symbol": "MID1",
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          "hgvs_c": "c.-111-1G>A",
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          "transcript": "ENST00000675358.1",
          "protein_id": "ENSP00000502220.1",
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        }
      ],
      "gene_symbol": "MID1",
      "gene_hgnc_id": 7095,
      "dbsnp": "rs1555895725",
      "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": 0.36000001430511475,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0.9380000233650208,
      "splice_prediction_selected": "Pathogenic",
      "splice_source_selected": "dbscSNV1_RF",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.36,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 7.377,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 1,
      "spliceai_max_prediction": "Pathogenic",
      "dbscsnv_ada_score": 0.999986675681007,
      "dbscsnv_ada_prediction": "Pathogenic",
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
      "acmg_by_gene": [
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PVS1_Moderate",
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000317552.9",
          "gene_symbol": "MID1",
          "hgnc_id": 7095,
          "effects": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "inheritance_mode": "XL",
          "hgvs_c": "c.757-1G>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "X-linked Opitz G/BBB syndrome",
      "clinvar_classification": "Likely pathogenic",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LP:1",
      "phenotype_combined": "X-linked Opitz G/BBB syndrome",
      "pathogenicity_classification_combined": "Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}