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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: 18-46521242-A-ACCAGCCAGCAGCT (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=46521242&ref=A&alt=ACCAGCCAGCAGCT&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "18",
      "pos": 46521242,
      "ref": "A",
      "alt": "ACCAGCCAGCAGCT",
      "effect": "frameshift_variant",
      "transcript": "ENST00000642948.1",
      "consequences": [
        {
          "aa_ref": "V",
          "aa_alt": "ELLAG?",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 33,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.5113_5125dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val1709fs",
          "transcript": "NM_001384474.1",
          "protein_id": "NP_001371403.1",
          "transcript_support_level": null,
          "aa_start": 1709,
          "aa_end": null,
          "aa_length": 2273,
          "cds_start": 5125,
          "cds_end": null,
          "cds_length": 6822,
          "cdna_start": 5312,
          "cdna_end": null,
          "cdna_length": 7208,
          "mane_select": "ENST00000642948.1",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "ELLAG?",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 33,
          "exon_rank_end": null,
          "exon_count": 41,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.5113_5125dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val1709fs",
          "transcript": "ENST00000642948.1",
          "protein_id": "ENSP00000496347.1",
          "transcript_support_level": null,
          "aa_start": 1709,
          "aa_end": null,
          "aa_length": 2273,
          "cds_start": 5125,
          "cds_end": null,
          "cds_length": 6822,
          "cdna_start": 5312,
          "cdna_end": null,
          "cdna_length": 7208,
          "mane_select": "NM_001384474.1",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "ELLAG?",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.1780_1792dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val598fs",
          "transcript": "ENST00000300591.11",
          "protein_id": "ENSP00000300591.6",
          "transcript_support_level": 1,
          "aa_start": 598,
          "aa_end": null,
          "aa_length": 1114,
          "cds_start": 1792,
          "cds_end": null,
          "cds_length": 3345,
          "cdna_start": 2206,
          "cdna_end": null,
          "cdna_length": 3968,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "ELLAG?",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.1492_1504dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val502fs",
          "transcript": "ENST00000579038.6",
          "protein_id": "ENSP00000463285.1",
          "transcript_support_level": 1,
          "aa_start": 502,
          "aa_end": null,
          "aa_length": 1011,
          "cds_start": 1504,
          "cds_end": null,
          "cds_length": 3036,
          "cdna_start": 1855,
          "cdna_end": null,
          "cdna_length": 3633,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "ELLAG?",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 31,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.4495_4507dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val1503fs",
          "transcript": "ENST00000441551.6",
          "protein_id": "ENSP00000387621.2",
          "transcript_support_level": 5,
          "aa_start": 1503,
          "aa_end": null,
          "aa_length": 2067,
          "cds_start": 4507,
          "cds_end": null,
          "cds_length": 6204,
          "cdna_start": 4507,
          "cdna_end": null,
          "cdna_length": 6226,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "ELLAG?",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.1780_1792dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val598fs",
          "transcript": "NM_001145472.3",
          "protein_id": "NP_001138944.1",
          "transcript_support_level": null,
          "aa_start": 598,
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          "aa_length": 1114,
          "cds_start": 1792,
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          "cdna_start": 2206,
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          "mane_select": null,
          "mane_plus": null,
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          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "ELLAG?",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.1492_1504dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val502fs",
          "transcript": "NM_001308013.2",
          "protein_id": "NP_001294942.1",
          "transcript_support_level": null,
          "aa_start": 502,
          "aa_end": null,
          "aa_length": 1011,
          "cds_start": 1504,
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          "cds_length": 3036,
          "cdna_start": 1855,
          "cdna_end": null,
          "cdna_length": 3644,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "ELLAG?",
          "canonical": false,
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          "strand": false,
          "consequences": [
            "frameshift_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 33,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.4069_4081dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val1361fs",
          "transcript": "XM_047437289.1",
          "protein_id": "XP_047293245.1",
          "transcript_support_level": null,
          "aa_start": 1361,
          "aa_end": null,
          "aa_length": 1925,
          "cds_start": 4081,
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          "cdna_start": 4180,
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          "mane_select": null,
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        },
        {
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          "consequences": [
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          ],
          "exon_rank": 26,
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          "exon_count": 33,
          "intron_rank": null,
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          "gene_symbol": "LOXHD1",
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          "hgvs_c": "c.4279_4291dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val1431fs",
          "transcript": "XM_047437290.1",
          "protein_id": "XP_047293246.1",
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        {
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          "intron_rank": null,
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          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3761,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": 25,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "n.4398+846_4398+858dupAGCTGCTGGCTGG",
          "hgvs_p": null,
          "transcript": "ENST00000335730.6",
          "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": 4775,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "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": 21,
          "intron_rank": 13,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.1884+846_1884+858dupAGCTGCTGGCTGG",
          "hgvs_p": null,
          "transcript": "XM_006722391.4",
          "protein_id": "XP_006722454.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1144,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3435,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3762,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LOXHD1",
          "gene_hgnc_id": 26521,
          "hgvs_c": "c.-919_-907dupAGCTGCTGGCTGG",
          "hgvs_p": null,
          "transcript": "XM_011525810.3",
          "protein_id": "XP_011524112.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 529,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 1590,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2499,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "LOXHD1",
      "gene_hgnc_id": 26521,
      "dbsnp": "rs876657855",
      "frequency_reference_population": 0.000026441641,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 37,
      "gnomad_exomes_af": 0.0000264416,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 37,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "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": 3.089,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": null,
      "spliceai_max_prediction": null,
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 7,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PVS1,BP6",
      "acmg_by_gene": [
        {
          "score": 7,
          "benign_score": 1,
          "pathogenic_score": 8,
          "criteria": [
            "PVS1",
            "BP6"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000642948.1",
          "gene_symbol": "LOXHD1",
          "hgnc_id": 26521,
          "effects": [
            "frameshift_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.5113_5125dupAGCTGCTGGCTGG",
          "hgvs_p": "p.Val1709fs"
        }
      ],
      "clinvar_disease": "not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:1 LB:1",
      "phenotype_combined": "not specified|not provided",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}