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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: 7-21901109-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=21901109&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "7",
      "pos": 21901109,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_001277115.2",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 82,
          "exon_rank_end": null,
          "exon_count": 82,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DNAH11",
          "gene_hgnc_id": 2942,
          "hgvs_c": "c.13406G>A",
          "hgvs_p": "p.Arg4469Lys",
          "transcript": "NM_001277115.2",
          "protein_id": "NP_001264044.1",
          "transcript_support_level": null,
          "aa_start": 4469,
          "aa_end": null,
          "aa_length": 4516,
          "cds_start": 13406,
          "cds_end": null,
          "cds_length": 13551,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000409508.8",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001277115.2"
        },
        {
          "aa_ref": "R",
          "aa_alt": "K",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 82,
          "exon_rank_end": null,
          "exon_count": 82,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DNAH11",
          "gene_hgnc_id": 2942,
          "hgvs_c": "c.13406G>A",
          "hgvs_p": "p.Arg4469Lys",
          "transcript": "ENST00000409508.8",
          "protein_id": "ENSP00000475939.1",
          "transcript_support_level": 5,
          "aa_start": 4469,
          "aa_end": null,
          "aa_length": 4516,
          "cds_start": 13406,
          "cds_end": null,
          "cds_length": 13551,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001277115.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000409508.8"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "NM_018719.5",
          "protein_id": "NP_061189.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 454,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1365,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000406877.8",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_018719.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "ENST00000406877.8",
          "protein_id": "ENSP00000383986.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 454,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1365,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_018719.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000406877.8"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "ENST00000934293.1",
          "protein_id": "ENSP00000604352.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 497,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1494,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000934293.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "ENST00000934292.1",
          "protein_id": "ENSP00000604351.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 484,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1455,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000934292.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "ENST00000943453.1",
          "protein_id": "ENSP00000613512.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 473,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1422,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000943453.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "ENST00000934295.1",
          "protein_id": "ENSP00000604354.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 460,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1383,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000934295.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "ENST00000904741.1",
          "protein_id": "ENSP00000574800.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 453,
          "cds_start": null,
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          "cds_length": 1362,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000904741.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
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          "transcript": "ENST00000934291.1",
          "protein_id": "ENSP00000604350.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 452,
          "cds_start": null,
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          "cdna_start": null,
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        },
        {
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          ],
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          "exon_count": 10,
          "intron_rank": null,
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          "gene_symbol": "CDCA7L",
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          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "ENST00000943457.1",
          "protein_id": "ENSP00000613516.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "cds_start": null,
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          "cdna_start": null,
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          "cds_start": null,
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        {
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        {
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          "gene_symbol": "CDCA7L",
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        {
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          ],
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          "gene_symbol": "CDCA7L",
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        {
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          "gene_symbol": "CDCA7L",
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          "hgvs_c": "c.*1213C>T",
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          "transcript": "ENST00000356195.9",
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        {
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        {
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          ],
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          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
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        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null,
          "transcript": "ENST00000904742.1",
          "protein_id": "ENSP00000574801.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 361,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1086,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000904742.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DNAH11",
          "gene_hgnc_id": 2942,
          "hgvs_c": "n.777G>A",
          "hgvs_p": null,
          "transcript": "ENST00000479878.1",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000479878.1"
        },
        {
          "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": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CDCA7L",
          "gene_hgnc_id": 30777,
          "hgvs_c": "n.1735C>T",
          "hgvs_p": null,
          "transcript": "ENST00000488845.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000488845.1"
        }
      ],
      "gene_symbol": "DNAH11",
      "gene_hgnc_id": 2942,
      "dbsnp": "rs183031009",
      "frequency_reference_population": 0.0002211885,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 357,
      "gnomad_exomes_af": 0.000130672,
      "gnomad_genomes_af": 0.00108975,
      "gnomad_exomes_ac": 191,
      "gnomad_genomes_ac": 166,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.004308134317398071,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.079,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1046,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.59,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 1.838,
      "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": -16,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1",
      "acmg_by_gene": [
        {
          "score": -16,
          "benign_score": 16,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BS1"
          ],
          "verdict": "Benign",
          "transcript": "NM_001277115.2",
          "gene_symbol": "DNAH11",
          "hgnc_id": 2942,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.13406G>A",
          "hgvs_p": "p.Arg4469Lys"
        },
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong"
          ],
          "verdict": "Benign",
          "transcript": "NM_018719.5",
          "gene_symbol": "CDCA7L",
          "hgnc_id": 30777,
          "effects": [
            "3_prime_UTR_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.*1213C>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "DNAH11-related disorder,Primary ciliary dyskinesia",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2",
      "phenotype_combined": "Primary ciliary dyskinesia|DNAH11-related disorder",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}