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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: 19-12948253-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12948253&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "19",
      "pos": 12948253,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_005053.4",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "NM_005053.4",
          "protein_id": "NP_005044.1",
          "transcript_support_level": null,
          "aa_start": 104,
          "aa_end": null,
          "aa_length": 363,
          "cds_start": 311,
          "cds_end": null,
          "cds_length": 1092,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000586534.6",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_005053.4"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "ENST00000586534.6",
          "protein_id": "ENSP00000467024.1",
          "transcript_support_level": 1,
          "aa_start": 104,
          "aa_end": null,
          "aa_length": 363,
          "cds_start": 311,
          "cds_end": null,
          "cds_length": 1092,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_005053.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000586534.6"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "ENST00000316856.7",
          "protein_id": "ENSP00000321365.3",
          "transcript_support_level": 1,
          "aa_start": 104,
          "aa_end": null,
          "aa_length": 362,
          "cds_start": 311,
          "cds_end": null,
          "cds_length": 1089,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000316856.7"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "NM_001270362.2",
          "protein_id": "NP_001257291.1",
          "transcript_support_level": null,
          "aa_start": 104,
          "aa_end": null,
          "aa_length": 362,
          "cds_start": 311,
          "cds_end": null,
          "cds_length": 1089,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001270362.2"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.305C>T",
          "hgvs_p": "p.Pro102Leu",
          "transcript": "ENST00000875551.1",
          "protein_id": "ENSP00000545610.1",
          "transcript_support_level": null,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 361,
          "cds_start": 305,
          "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": "ENST00000875551.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "ENST00000925763.1",
          "protein_id": "ENSP00000595822.1",
          "transcript_support_level": null,
          "aa_start": 104,
          "aa_end": null,
          "aa_length": 361,
          "cds_start": 311,
          "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": "ENST00000925763.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.305C>T",
          "hgvs_p": "p.Pro102Leu",
          "transcript": "ENST00000875552.1",
          "protein_id": "ENSP00000545611.1",
          "transcript_support_level": null,
          "aa_start": 102,
          "aa_end": null,
          "aa_length": 360,
          "cds_start": 305,
          "cds_end": null,
          "cds_length": 1083,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000875552.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "ENST00000875556.1",
          "protein_id": "ENSP00000545615.1",
          "transcript_support_level": null,
          "aa_start": 104,
          "aa_end": null,
          "aa_length": 356,
          "cds_start": 311,
          "cds_end": null,
          "cds_length": 1071,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000875556.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "ENST00000943230.1",
          "protein_id": "ENSP00000613289.1",
          "transcript_support_level": null,
          "aa_start": 104,
          "aa_end": null,
          "aa_length": 355,
          "cds_start": 311,
          "cds_end": null,
          "cds_length": 1068,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000943230.1"
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "ENST00000875559.1",
          "protein_id": "ENSP00000545618.1",
          "transcript_support_level": null,
          "aa_start": 104,
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          "aa_length": 352,
          "cds_start": 311,
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          "cdna_start": null,
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        {
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          ],
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          "exon_count": 9,
          "intron_rank": null,
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          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu",
          "transcript": "ENST00000925765.1",
          "protein_id": "ENSP00000595824.1",
          "transcript_support_level": null,
          "aa_start": 104,
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          "aa_length": 349,
          "cds_start": 311,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
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        {
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          "intron_rank": null,
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          "transcript": "ENST00000875557.1",
          "protein_id": "ENSP00000545616.1",
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        {
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        {
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          ],
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          "exon_count": 9,
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          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
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        {
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        {
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          "gene_symbol": "RAD23A",
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          "transcript": "NM_001270363.2",
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        {
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          "gene_symbol": "RAD23A",
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          "hgvs_c": "c.311C>T",
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          "transcript": "ENST00000592268.5",
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        {
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        {
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          ],
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          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "c.235-18C>T",
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          "transcript": "ENST00000925764.1",
          "protein_id": "ENSP00000595823.1",
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          "intron_rank": null,
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          "transcript": "ENST00000588826.2",
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        {
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          "exon_count": 8,
          "intron_rank": null,
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          "gene_symbol": "RAD23A",
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          "hgvs_c": "n.311C>T",
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          "transcript": "ENST00000591499.5",
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          "transcript_support_level": 2,
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          "cdna_start": null,
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          "biotype": "nonsense_mediated_decay",
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        {
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          "consequences": [
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          "exon_count": 9,
          "intron_rank": null,
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          "gene_symbol": "RAD23A",
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          "transcript": "ENST00000593114.5",
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          "biotype": "nonsense_mediated_decay",
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        {
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
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          "intron_rank": null,
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          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "n.311C>T",
          "hgvs_p": null,
          "transcript": "ENST00000651137.1",
          "protein_id": "ENSP00000498473.1",
          "transcript_support_level": null,
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          "mane_select": null,
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          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000651137.1"
        },
        {
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
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          "exon_count": 8,
          "intron_rank": null,
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          "gene_symbol": "RAD23A",
          "gene_hgnc_id": 9812,
          "hgvs_c": "n.398C>T",
          "hgvs_p": null,
          "transcript": "NR_072976.2",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "pseudogene",
          "feature": "NR_072976.2"
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      ],
      "gene_symbol": "RAD23A",
      "gene_hgnc_id": 9812,
      "dbsnp": "rs375981873",
      "frequency_reference_population": 0.000071880124,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 116,
      "gnomad_exomes_af": 0.0000690999,
      "gnomad_genomes_af": 0.0000985895,
      "gnomad_exomes_ac": 101,
      "gnomad_genomes_ac": 15,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.029682159423828125,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.042,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0723,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.68,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.495,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.01,
      "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": -6,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Strong,BP6_Moderate",
      "acmg_by_gene": [
        {
          "score": -6,
          "benign_score": 6,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Moderate"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_005053.4",
          "gene_symbol": "RAD23A",
          "hgnc_id": 9812,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.311C>T",
          "hgvs_p": "p.Pro104Leu"
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LB:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}