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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: 20-8733357-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=8733357&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "20",
      "pos": 8733357,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000338037.11",
      "consequences": [
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "c.2008G>A",
          "hgvs_p": "p.Val670Ile",
          "transcript": "NM_015192.4",
          "protein_id": "NP_056007.1",
          "transcript_support_level": null,
          "aa_start": 670,
          "aa_end": null,
          "aa_length": 1216,
          "cds_start": 2008,
          "cds_end": null,
          "cds_length": 3651,
          "cdna_start": 2394,
          "cdna_end": null,
          "cdna_length": 7088,
          "mane_select": "ENST00000338037.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "c.2008G>A",
          "hgvs_p": "p.Val670Ile",
          "transcript": "ENST00000338037.11",
          "protein_id": "ENSP00000338185.6",
          "transcript_support_level": 1,
          "aa_start": 670,
          "aa_end": null,
          "aa_length": 1216,
          "cds_start": 2008,
          "cds_end": null,
          "cds_length": 3651,
          "cdna_start": 2394,
          "cdna_end": null,
          "cdna_length": 7088,
          "mane_select": "NM_015192.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "c.2008G>A",
          "hgvs_p": "p.Val670Ile",
          "transcript": "ENST00000378637.6",
          "protein_id": "ENSP00000367904.2",
          "transcript_support_level": 1,
          "aa_start": 670,
          "aa_end": null,
          "aa_length": 1173,
          "cds_start": 2008,
          "cds_end": null,
          "cds_length": 3522,
          "cdna_start": 2011,
          "cdna_end": null,
          "cdna_length": 3864,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 33,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "c.2008G>A",
          "hgvs_p": "p.Val670Ile",
          "transcript": "ENST00000378641.7",
          "protein_id": "ENSP00000367908.3",
          "transcript_support_level": 1,
          "aa_start": 670,
          "aa_end": null,
          "aa_length": 1173,
          "cds_start": 2008,
          "cds_end": null,
          "cds_length": 3522,
          "cdna_start": 2522,
          "cdna_end": null,
          "cdna_length": 7323,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "n.1228G>A",
          "hgvs_p": null,
          "transcript": "ENST00000487210.5",
          "protein_id": "ENSP00000431704.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4781,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 33,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "c.2008G>A",
          "hgvs_p": "p.Val670Ile",
          "transcript": "NM_182734.3",
          "protein_id": "NP_877398.1",
          "transcript_support_level": null,
          "aa_start": 670,
          "aa_end": null,
          "aa_length": 1173,
          "cds_start": 2008,
          "cds_end": null,
          "cds_length": 3522,
          "cdna_start": 2394,
          "cdna_end": null,
          "cdna_length": 7206,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 33,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "c.1705G>A",
          "hgvs_p": "p.Val569Ile",
          "transcript": "ENST00000637919.1",
          "protein_id": "ENSP00000490862.1",
          "transcript_support_level": 5,
          "aa_start": 569,
          "aa_end": null,
          "aa_length": 1072,
          "cds_start": 1705,
          "cds_end": null,
          "cds_length": 3219,
          "cdna_start": 1963,
          "cdna_end": null,
          "cdna_length": 5074,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "c.1705G>A",
          "hgvs_p": "p.Val569Ile",
          "transcript": "ENST00000626966.2",
          "protein_id": "ENSP00000487075.1",
          "transcript_support_level": 2,
          "aa_start": 569,
          "aa_end": null,
          "aa_length": 960,
          "cds_start": 1705,
          "cds_end": null,
          "cds_length": 2883,
          "cdna_start": 1818,
          "cdna_end": null,
          "cdna_length": 2996,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "c.1705G>A",
          "hgvs_p": "p.Val569Ile",
          "transcript": "ENST00000625874.2",
          "protein_id": "ENSP00000486301.1",
          "transcript_support_level": 2,
          "aa_start": 569,
          "aa_end": null,
          "aa_length": 959,
          "cds_start": 1705,
          "cds_end": null,
          "cds_length": 2881,
          "cdna_start": 2030,
          "cdna_end": null,
          "cdna_length": 3206,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "n.1160G>A",
          "hgvs_p": null,
          "transcript": "ENST00000494924.2",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2338,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "n.2079G>A",
          "hgvs_p": null,
          "transcript": "ENST00000635830.1",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3237,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "n.1872G>A",
          "hgvs_p": null,
          "transcript": "ENST00000636825.1",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3020,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PLCB1",
          "gene_hgnc_id": 15917,
          "hgvs_c": "n.*84G>A",
          "hgvs_p": null,
          "transcript": "ENST00000636711.1",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 100,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PLCB1",
      "gene_hgnc_id": 15917,
      "dbsnp": "rs772981786",
      "frequency_reference_population": 0.000008209248,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 12,
      "gnomad_exomes_af": 0.00000820925,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 12,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.2256823480129242,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.019999999552965164,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.141,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1368,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.39,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 8.149,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0.02,
      "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": -2,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Moderate",
      "acmg_by_gene": [
        {
          "score": -2,
          "benign_score": 2,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000338037.11",
          "gene_symbol": "PLCB1",
          "hgnc_id": 15917,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.2008G>A",
          "hgvs_p": "p.Val670Ile"
        }
      ],
      "clinvar_disease": " 12,Developmental and epileptic encephalopathy",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "Developmental and epileptic encephalopathy, 12",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}