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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: 10-97451724-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=97451724&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "10",
      "pos": 97451724,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_032327.4",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "NM_198046.3",
          "protein_id": "NP_932163.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 377,
          "cds_start": 49,
          "cds_end": null,
          "cds_length": 1134,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000393760.6",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_198046.3"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000393760.6",
          "protein_id": "ENSP00000377357.1",
          "transcript_support_level": 1,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 377,
          "cds_start": 49,
          "cds_end": null,
          "cds_length": 1134,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_198046.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000393760.6"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000370854.7",
          "protein_id": "ENSP00000359891.3",
          "transcript_support_level": 1,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 377,
          "cds_start": 49,
          "cds_end": null,
          "cds_length": 1134,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000370854.7"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000352634.8",
          "protein_id": "ENSP00000345383.4",
          "transcript_support_level": 1,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 361,
          "cds_start": 49,
          "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": "ENST00000352634.8"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000353979.7",
          "protein_id": "ENSP00000323360.3",
          "transcript_support_level": 1,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 338,
          "cds_start": 49,
          "cds_end": null,
          "cds_length": 1017,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000353979.7"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000345745.9",
          "protein_id": "ENSP00000304487.8",
          "transcript_support_level": 1,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 296,
          "cds_start": 49,
          "cds_end": null,
          "cds_length": 891,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000345745.9"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000862048.1",
          "protein_id": "ENSP00000532107.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 384,
          "cds_start": 49,
          "cds_end": null,
          "cds_length": 1155,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000862048.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "NM_032327.4",
          "protein_id": "NP_115703.2",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 377,
          "cds_start": 49,
          "cds_end": null,
          "cds_length": 1134,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_032327.4"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000951312.1",
          "protein_id": "ENSP00000621371.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 377,
          "cds_start": 49,
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          "cds_length": 1134,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000951312.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000951305.1",
          "protein_id": "ENSP00000621364.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 376,
          "cds_start": 49,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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        },
        {
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          "consequences": [
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          ],
          "exon_rank": 2,
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          "exon_count": 10,
          "intron_rank": null,
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          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "NM_198043.3",
          "protein_id": "NP_932160.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 361,
          "cds_start": 49,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_198043.3"
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        {
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 3,
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          "intron_rank": null,
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          "gene_symbol": "ZDHHC16",
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          "hgvs_c": "c.49C>T",
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          "transcript": "ENST00000370842.6",
          "protein_id": "ENSP00000359879.1",
          "transcript_support_level": 5,
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          "cds_start": 49,
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          "cdna_start": null,
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          "biotype": "protein_coding",
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        },
        {
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 1,
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          "intron_rank": null,
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          "gene_symbol": "ZDHHC16",
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          "hgvs_c": "c.49C>T",
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          "transcript": "ENST00000862058.1",
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          "biotype": "protein_coding",
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        {
          "aa_ref": "R",
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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": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000916030.1",
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        {
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          "hgvs_c": "c.49C>T",
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          "transcript": "ENST00000916031.1",
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          "biotype": "protein_coding",
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        {
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          "intron_rank": null,
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          "gene_symbol": "ZDHHC16",
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          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "ENST00000951308.1",
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        {
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          "intron_rank": null,
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          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "NM_001287803.2",
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        {
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        {
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          "biotype": "protein_coding",
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        },
        {
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          ],
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          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ZDHHC16",
          "gene_hgnc_id": 20714,
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys",
          "transcript": "NM_198044.3",
          "protein_id": "NP_932161.1",
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        {
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          "transcript": "ENST00000417044.1",
          "protein_id": "ENSP00000396286.1",
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          "biotype": "protein_coding",
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        },
        {
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          "protein_coding": false,
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          "consequences": [
            "upstream_gene_variant"
          ],
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          "gene_symbol": "ZDHHC16",
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          "hgvs_c": "n.-12C>T",
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          "transcript": "ENST00000495735.5",
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          "biotype": "pseudogene",
          "feature": "ENST00000495735.5"
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      ],
      "gene_symbol": "ZDHHC16",
      "gene_hgnc_id": 20714,
      "dbsnp": "rs376949987",
      "frequency_reference_population": 0.00013389453,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 216,
      "gnomad_exomes_af": 0.000143057,
      "gnomad_genomes_af": 0.0000459746,
      "gnomad_exomes_ac": 209,
      "gnomad_genomes_ac": 7,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.2675629258155823,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.11999999731779099,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.192,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.4477,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.14,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 2.2,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.12,
      "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": -1,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4",
      "acmg_by_gene": [
        {
          "score": -1,
          "benign_score": 1,
          "pathogenic_score": 0,
          "criteria": [
            "BP4"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_032327.4",
          "gene_symbol": "ZDHHC16",
          "hgnc_id": 20714,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.49C>T",
          "hgvs_p": "p.Arg17Cys"
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}