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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: 2-227059468-C-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227059468&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 227059468,
      "ref": "C",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000396625.5",
      "consequences": [
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 48,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "NM_000092.5",
          "protein_id": "NP_000083.3",
          "transcript_support_level": null,
          "aa_start": 774,
          "aa_end": null,
          "aa_length": 1690,
          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 5073,
          "cdna_start": 2620,
          "cdna_end": null,
          "cdna_length": 9984,
          "mane_select": "ENST00000396625.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 48,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "ENST00000396625.5",
          "protein_id": "ENSP00000379866.3",
          "transcript_support_level": 5,
          "aa_start": 774,
          "aa_end": null,
          "aa_length": 1690,
          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 5073,
          "cdna_start": 2620,
          "cdna_end": null,
          "cdna_length": 9984,
          "mane_select": "NM_000092.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 48,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "XM_005246281.4",
          "protein_id": "XP_005246338.1",
          "transcript_support_level": null,
          "aa_start": 774,
          "aa_end": null,
          "aa_length": 1690,
          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 5073,
          "cdna_start": 2514,
          "cdna_end": null,
          "cdna_length": 9878,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 48,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "XM_047443228.1",
          "protein_id": "XP_047299184.1",
          "transcript_support_level": null,
          "aa_start": 774,
          "aa_end": null,
          "aa_length": 1690,
          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 5073,
          "cdna_start": 2497,
          "cdna_end": null,
          "cdna_length": 9861,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 49,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "XM_011510557.3",
          "protein_id": "XP_011508859.1",
          "transcript_support_level": null,
          "aa_start": 774,
          "aa_end": null,
          "aa_length": 1663,
          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 4992,
          "cdna_start": 2620,
          "cdna_end": null,
          "cdna_length": 9903,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 27,
          "exon_rank_end": null,
          "exon_count": 47,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2212G>C",
          "hgvs_p": "p.Gly738Arg",
          "transcript": "XM_011510558.3",
          "protein_id": "XP_011508860.1",
          "transcript_support_level": null,
          "aa_start": 738,
          "aa_end": null,
          "aa_length": 1654,
          "cds_start": 2212,
          "cds_end": null,
          "cds_length": 4965,
          "cdna_start": 2512,
          "cdna_end": null,
          "cdna_length": 9876,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 48,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "XM_017003297.2",
          "protein_id": "XP_016858786.1",
          "transcript_support_level": null,
          "aa_start": 774,
          "aa_end": null,
          "aa_length": 1651,
          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 4956,
          "cdna_start": 2620,
          "cdna_end": null,
          "cdna_length": 9867,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 47,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "XM_006712246.4",
          "protein_id": "XP_006712309.1",
          "transcript_support_level": null,
          "aa_start": 774,
          "aa_end": null,
          "aa_length": 1627,
          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 4884,
          "cdna_start": 2620,
          "cdna_end": null,
          "cdna_length": 9795,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 49,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "XM_011510559.3",
          "protein_id": "XP_011508861.1",
          "transcript_support_level": null,
          "aa_start": 774,
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          "cds_start": 2320,
          "cds_end": null,
          "cds_length": 4839,
          "cdna_start": 2620,
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          "cdna_length": 6050,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "G",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 28,
          "exon_rank_end": null,
          "exon_count": 49,
          "intron_rank": null,
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          "gene_symbol": "COL4A4",
          "gene_hgnc_id": 2206,
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
          "transcript": "XM_011510560.3",
          "protein_id": "XP_011508862.1",
          "transcript_support_level": null,
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          "cds_start": 2320,
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        {
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          "gene_symbol": "COL4A4",
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          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg",
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        {
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        {
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        {
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        {
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          "transcript": "XM_005246282.4",
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        {
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      ],
      "gene_symbol": "COL4A4",
      "gene_hgnc_id": 2206,
      "dbsnp": "rs569681869",
      "frequency_reference_population": 0.000042131873,
      "hom_count_reference_population": 1,
      "allele_count_reference_population": 68,
      "gnomad_exomes_af": 0.000043095,
      "gnomad_genomes_af": 0.0000328748,
      "gnomad_exomes_ac": 63,
      "gnomad_genomes_ac": 5,
      "gnomad_exomes_homalt": 1,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9942065477371216,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.05999999865889549,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.957,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.8951,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.54,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 5.101,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0.06,
      "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": 9,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM1,PM5,PP3_Strong,PP5",
      "acmg_by_gene": [
        {
          "score": 9,
          "benign_score": 0,
          "pathogenic_score": 9,
          "criteria": [
            "PM1",
            "PM5",
            "PP3_Strong",
            "PP5"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000396625.5",
          "gene_symbol": "COL4A4",
          "hgnc_id": 2206,
          "effects": [
            "missense_variant"
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          "inheritance_mode": "AR,AD,SD",
          "hgvs_c": "c.2320G>C",
          "hgvs_p": "p.Gly774Arg"
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      ],
      "clinvar_disease": " 1, benign familial,Alport syndrome,Autosomal recessive Alport syndrome,Benign familial hematuria,Hearing impairment,Hematuria,Hypertensive disorder,Myopia,Proteinuria,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "P:7 LP:5 US:1",
      "phenotype_combined": "Myopia;Hypertensive disorder;Hematuria;Proteinuria;Hearing impairment|Autosomal recessive Alport syndrome|Alport syndrome|not provided|Benign familial hematuria|Autosomal recessive Alport syndrome;Hematuria, benign familial, 1",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}