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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: 3-197681350-G-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=197681350&ref=G&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 197681350,
      "ref": "G",
      "alt": "T",
      "effect": "synonymous_variant",
      "transcript": "ENST00000296343.10",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2209C>A",
          "hgvs_p": "p.Arg737Arg",
          "transcript": "NM_014687.4",
          "protein_id": "NP_055502.1",
          "transcript_support_level": null,
          "aa_start": 737,
          "aa_end": null,
          "aa_length": 972,
          "cds_start": 2209,
          "cds_end": null,
          "cds_length": 2919,
          "cdna_start": 2394,
          "cdna_end": null,
          "cdna_length": 9255,
          "mane_select": "ENST00000296343.10",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2209C>A",
          "hgvs_p": "p.Arg737Arg",
          "transcript": "ENST00000296343.10",
          "protein_id": "ENSP00000296343.5",
          "transcript_support_level": 1,
          "aa_start": 737,
          "aa_end": null,
          "aa_length": 972,
          "cds_start": 2209,
          "cds_end": null,
          "cds_length": 2919,
          "cdna_start": 2394,
          "cdna_end": null,
          "cdna_length": 9255,
          "mane_select": "NM_014687.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.1558C>A",
          "hgvs_p": "p.Arg520Arg",
          "transcript": "ENST00000415452.5",
          "protein_id": "ENSP00000409618.1",
          "transcript_support_level": 1,
          "aa_start": 520,
          "aa_end": null,
          "aa_length": 679,
          "cds_start": 1558,
          "cds_end": null,
          "cds_length": 2040,
          "cdna_start": 1560,
          "cdna_end": null,
          "cdna_length": 2665,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2326C>A",
          "hgvs_p": "p.Arg776Arg",
          "transcript": "NM_001346873.2",
          "protein_id": "NP_001333802.1",
          "transcript_support_level": null,
          "aa_start": 776,
          "aa_end": null,
          "aa_length": 1011,
          "cds_start": 2326,
          "cds_end": null,
          "cds_length": 3036,
          "cdna_start": 2511,
          "cdna_end": null,
          "cdna_length": 9372,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2326C>A",
          "hgvs_p": "p.Arg776Arg",
          "transcript": "ENST00000707076.1",
          "protein_id": "ENSP00000516727.1",
          "transcript_support_level": null,
          "aa_start": 776,
          "aa_end": null,
          "aa_length": 1011,
          "cds_start": 2326,
          "cds_end": null,
          "cds_length": 3036,
          "cdna_start": 2508,
          "cdna_end": null,
          "cdna_length": 3218,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2092C>A",
          "hgvs_p": "p.Arg698Arg",
          "transcript": "ENST00000413360.5",
          "protein_id": "ENSP00000405115.1",
          "transcript_support_level": 5,
          "aa_start": 698,
          "aa_end": null,
          "aa_length": 933,
          "cds_start": 2092,
          "cds_end": null,
          "cds_length": 2802,
          "cdna_start": 2093,
          "cdna_end": null,
          "cdna_length": 3801,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2074C>A",
          "hgvs_p": "p.Arg692Arg",
          "transcript": "NM_001145642.5",
          "protein_id": "NP_001139114.1",
          "transcript_support_level": null,
          "aa_start": 692,
          "aa_end": null,
          "aa_length": 927,
          "cds_start": 2074,
          "cds_end": null,
          "cds_length": 2784,
          "cdna_start": 2741,
          "cdna_end": null,
          "cdna_length": 9602,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2074C>A",
          "hgvs_p": "p.Arg692Arg",
          "transcript": "ENST00000273582.9",
          "protein_id": "ENSP00000273582.5",
          "transcript_support_level": 5,
          "aa_start": 692,
          "aa_end": null,
          "aa_length": 927,
          "cds_start": 2074,
          "cds_end": null,
          "cds_length": 2784,
          "cdna_start": 2620,
          "cdna_end": null,
          "cdna_length": 6955,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2329C>A",
          "hgvs_p": "p.Arg777Arg",
          "transcript": "XM_006713827.4",
          "protein_id": "XP_006713890.1",
          "transcript_support_level": null,
          "aa_start": 777,
          "aa_end": null,
          "aa_length": 1012,
          "cds_start": 2329,
          "cds_end": null,
          "cds_length": 3039,
          "cdna_start": 2514,
          "cdna_end": null,
          "cdna_length": 9375,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2284C>A",
          "hgvs_p": "p.Arg762Arg",
          "transcript": "XM_006713828.4",
          "protein_id": "XP_006713891.1",
          "transcript_support_level": null,
          "aa_start": 762,
          "aa_end": null,
          "aa_length": 997,
          "cds_start": 2284,
          "cds_end": null,
          "cds_length": 2994,
          "cdna_start": 2469,
          "cdna_end": null,
          "cdna_length": 9330,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2266C>A",
          "hgvs_p": "p.Arg756Arg",
          "transcript": "XM_047449268.1",
          "protein_id": "XP_047305224.1",
          "transcript_support_level": null,
          "aa_start": 756,
          "aa_end": null,
          "aa_length": 991,
          "cds_start": 2266,
          "cds_end": null,
          "cds_length": 2976,
          "cdna_start": 2940,
          "cdna_end": null,
          "cdna_length": 9801,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.2254C>A",
          "hgvs_p": "p.Arg752Arg",
          "transcript": "XM_005269374.4",
          "protein_id": "XP_005269431.1",
          "transcript_support_level": null,
          "aa_start": 752,
          "aa_end": null,
          "aa_length": 987,
          "cds_start": 2254,
          "cds_end": null,
          "cds_length": 2964,
          "cdna_start": 2439,
          "cdna_end": null,
          "cdna_length": 9300,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.1828C>A",
          "hgvs_p": "p.Arg610Arg",
          "transcript": "XM_006713831.5",
          "protein_id": "XP_006713894.1",
          "transcript_support_level": null,
          "aa_start": 610,
          "aa_end": null,
          "aa_length": 845,
          "cds_start": 1828,
          "cds_end": null,
          "cds_length": 2538,
          "cdna_start": 2662,
          "cdna_end": null,
          "cdna_length": 9523,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RUBCN",
          "gene_hgnc_id": 28991,
          "hgvs_c": "c.1783C>A",
          "hgvs_p": "p.Arg595Arg",
          "transcript": "XM_017007543.2",
          "protein_id": "XP_016863032.1",
          "transcript_support_level": null,
          "aa_start": 595,
          "aa_end": null,
          "aa_length": 830,
          "cds_start": 1783,
          "cds_end": null,
          "cds_length": 2493,
          "cdna_start": 2315,
          "cdna_end": null,
          "cdna_length": 9176,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "RUBCN",
      "gene_hgnc_id": 28991,
      "dbsnp": "rs770720829",
      "frequency_reference_population": 0.0000068512013,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 10,
      "gnomad_exomes_af": 0.0000068512,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 10,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.7990000247955322,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "REVEL",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.799,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.35,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 8.039,
      "phylop100way_prediction": "Pathogenic",
      "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": 4,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PP3_Moderate",
      "acmg_by_gene": [
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PP3_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000296343.10",
          "gene_symbol": "RUBCN",
          "hgnc_id": 28991,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.2209C>A",
          "hgvs_p": "p.Arg737Arg"
        }
      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}