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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: 3-9428989-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=9428989&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 9428989,
      "ref": "A",
      "alt": "G",
      "effect": "synonymous_variant",
      "transcript": "NM_001080517.3",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "NM_001080517.3",
          "protein_id": "NP_001073986.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1442,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4329,
          "cdna_start": 590,
          "cdna_end": null,
          "cdna_length": 6931,
          "mane_select": "ENST00000402198.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "ENST00000402198.7",
          "protein_id": "ENSP00000385852.2",
          "transcript_support_level": 5,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1442,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4329,
          "cdna_start": 590,
          "cdna_end": null,
          "cdna_length": 6931,
          "mane_select": "NM_001080517.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "NM_001437635.1",
          "protein_id": "NP_001424564.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1480,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4443,
          "cdna_start": 590,
          "cdna_end": null,
          "cdna_length": 7037,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "NM_001437633.1",
          "protein_id": "NP_001424562.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1474,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4425,
          "cdna_start": 590,
          "cdna_end": null,
          "cdna_length": 7019,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "ENST00000682536.1",
          "protein_id": "ENSP00000507956.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1474,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4425,
          "cdna_start": 324,
          "cdna_end": null,
          "cdna_length": 5624,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "NM_001437643.1",
          "protein_id": "NP_001424572.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1461,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4386,
          "cdna_start": 1125,
          "cdna_end": null,
          "cdna_length": 7515,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "ENST00000407969.5",
          "protein_id": "ENSP00000384114.1",
          "transcript_support_level": 5,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1461,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4386,
          "cdna_start": 65,
          "cdna_end": null,
          "cdna_length": 6463,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "NM_001437701.1",
          "protein_id": "NP_001424630.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1455,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4368,
          "cdna_start": 590,
          "cdna_end": null,
          "cdna_length": 6962,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "ENST00000406341.5",
          "protein_id": "ENSP00000383939.1",
          "transcript_support_level": 5,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 1442,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 4329,
          "cdna_start": 241,
          "cdna_end": null,
          "cdna_length": 6582,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "ENST00000684055.1",
          "protein_id": "ENSP00000507953.1",
          "transcript_support_level": null,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 931,
          "cds_start": 51,
          "cds_end": null,
          "cds_length": 2796,
          "cdna_start": 167,
          "cdna_end": null,
          "cdna_length": 4416,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
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          "exon_count": 4,
          "intron_rank": null,
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          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "ENST00000468208.2",
          "protein_id": "ENSP00000499609.1",
          "transcript_support_level": 3,
          "aa_start": 17,
          "aa_end": null,
          "aa_length": 52,
          "cds_start": 51,
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          "cds_length": 159,
          "cdna_start": 390,
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          "cdna_length": 1415,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
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          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "XM_011533922.2",
          "protein_id": "XP_011532224.1",
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          "mane_select": null,
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        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 4,
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          "exon_count": 26,
          "intron_rank": null,
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          "gene_symbol": "SETD5",
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          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "XM_047448473.1",
          "protein_id": "XP_047304429.1",
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        },
        {
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          "exon_count": 25,
          "intron_rank": null,
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          "gene_symbol": "SETD5",
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          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "XM_047448474.1",
          "protein_id": "XP_047304430.1",
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          "mane_select": null,
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          "feature": null
        },
        {
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          "aa_alt": "S",
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          ],
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          "gene_symbol": "SETD5",
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        {
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          "consequences": [
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          "intron_rank": null,
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          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "XM_047448479.1",
          "protein_id": "XP_047304435.1",
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        {
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          "strand": true,
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          "exon_rank": 3,
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          "gene_symbol": "SETD5",
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          "hgvs_c": "c.51A>G",
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          "mane_select": null,
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        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
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          "protein_coding": true,
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          ],
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          "gene_symbol": "SETD5",
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        {
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          "strand": true,
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          "gene_symbol": "SETD5",
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          "hgvs_c": "c.51A>G",
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        },
        {
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          "consequences": [
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          ],
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          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
          "transcript": "XM_005265301.2",
          "protein_id": "XP_005265358.1",
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          "cdna_length": 6988,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 3,
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          "exon_count": 24,
          "intron_rank": null,
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          "gene_symbol": "SETD5",
          "gene_hgnc_id": 25566,
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser",
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        {
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      ],
      "gene_symbol": "SETD5",
      "gene_hgnc_id": 25566,
      "dbsnp": "rs1394101476",
      "frequency_reference_population": 0.0000020537732,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 3,
      "gnomad_exomes_af": 0.00000205377,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 3,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.5400000214576721,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.54,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 1.765,
      "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": -3,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PM2,BP4_Strong,BP7",
      "acmg_by_gene": [
        {
          "score": -3,
          "benign_score": 5,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong",
            "BP7"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_001080517.3",
          "gene_symbol": "SETD5",
          "hgnc_id": 25566,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.51A>G",
          "hgvs_p": "p.Ser17Ser"
        }
      ],
      "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
}