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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: 15-89333725-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=89333725&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "15",
      "pos": 89333725,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000706918.1",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLGARF",
          "gene_hgnc_id": 56246,
          "hgvs_c": "c.85C>T",
          "hgvs_p": "p.Arg29Trp",
          "transcript": "ENST00000706918.1",
          "protein_id": "ENSP00000516626.1",
          "transcript_support_level": null,
          "aa_start": 29,
          "aa_end": null,
          "aa_length": 260,
          "cds_start": 85,
          "cds_end": null,
          "cds_length": 783,
          "cdna_start": 85,
          "cdna_end": null,
          "cdna_length": 783,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "c.30C>T",
          "hgvs_p": "p.Ala10Ala",
          "transcript": "NM_002693.3",
          "protein_id": "NP_002684.1",
          "transcript_support_level": null,
          "aa_start": 10,
          "aa_end": null,
          "aa_length": 1239,
          "cds_start": 30,
          "cds_end": null,
          "cds_length": 3720,
          "cdna_start": 341,
          "cdna_end": null,
          "cdna_length": 4462,
          "mane_select": "ENST00000268124.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "c.30C>T",
          "hgvs_p": "p.Ala10Ala",
          "transcript": "ENST00000268124.11",
          "protein_id": "ENSP00000268124.5",
          "transcript_support_level": 1,
          "aa_start": 10,
          "aa_end": null,
          "aa_length": 1239,
          "cds_start": 30,
          "cds_end": null,
          "cds_length": 3720,
          "cdna_start": 341,
          "cdna_end": null,
          "cdna_length": 4462,
          "mane_select": "NM_002693.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "c.30C>T",
          "hgvs_p": "p.Ala10Ala",
          "transcript": "ENST00000442287.6",
          "protein_id": "ENSP00000399851.2",
          "transcript_support_level": 1,
          "aa_start": 10,
          "aa_end": null,
          "aa_length": 1239,
          "cds_start": 30,
          "cds_end": null,
          "cds_length": 3720,
          "cdna_start": 366,
          "cdna_end": null,
          "cdna_length": 4487,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLGARF",
          "gene_hgnc_id": 56246,
          "hgvs_c": "c.85C>T",
          "hgvs_p": "p.Arg29Trp",
          "transcript": "NM_001430120.1",
          "protein_id": "NP_001417049.1",
          "transcript_support_level": null,
          "aa_start": 29,
          "aa_end": null,
          "aa_length": 260,
          "cds_start": 85,
          "cds_end": null,
          "cds_length": 783,
          "cdna_start": 85,
          "cdna_end": null,
          "cdna_length": 783,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "c.30C>T",
          "hgvs_p": "p.Ala10Ala",
          "transcript": "NM_001126131.2",
          "protein_id": "NP_001119603.1",
          "transcript_support_level": null,
          "aa_start": 10,
          "aa_end": null,
          "aa_length": 1239,
          "cds_start": 30,
          "cds_end": null,
          "cds_length": 3720,
          "cdna_start": 329,
          "cdna_end": null,
          "cdna_length": 4450,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "c.30C>T",
          "hgvs_p": "p.Ala10Ala",
          "transcript": "ENST00000636937.2",
          "protein_id": "ENSP00000516154.1",
          "transcript_support_level": 5,
          "aa_start": 10,
          "aa_end": null,
          "aa_length": 1239,
          "cds_start": 30,
          "cds_end": null,
          "cds_length": 3720,
          "cdna_start": 974,
          "cdna_end": null,
          "cdna_length": 5095,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "n.30C>T",
          "hgvs_p": null,
          "transcript": "ENST00000631044.2",
          "protein_id": "ENSP00000486730.1",
          "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": 4668,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "n.30C>T",
          "hgvs_p": null,
          "transcript": "ENST00000635986.2",
          "protein_id": "ENSP00000490653.2",
          "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": 4388,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "n.30C>T",
          "hgvs_p": null,
          "transcript": "ENST00000636774.1",
          "protein_id": "ENSP00000489799.1",
          "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": 4151,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "n.228C>T",
          "hgvs_p": null,
          "transcript": "ENST00000672071.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 5318,
          "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": "POLG",
          "gene_hgnc_id": 9179,
          "hgvs_c": "n.*125C>T",
          "hgvs_p": null,
          "transcript": "ENST00000637711.1",
          "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": 142,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "POLGARF",
      "gene_hgnc_id": 56246,
      "dbsnp": "rs1060504037",
      "frequency_reference_population": 0.000013021901,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 20,
      "gnomad_exomes_af": 0.0000130082,
      "gnomad_genomes_af": 0.0000131461,
      "gnomad_exomes_ac": 18,
      "gnomad_genomes_ac": 2,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.055162638425827026,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": "Uncertain_significance",
      "bayesdelnoaf_score": -0.55,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.067,
      "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": -12,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong",
      "acmg_by_gene": [
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000706918.1",
          "gene_symbol": "POLGARF",
          "hgnc_id": 56246,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.85C>T",
          "hgvs_p": "p.Arg29Trp"
        },
        {
          "score": -13,
          "benign_score": 13,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000268124.11",
          "gene_symbol": "POLG",
          "hgnc_id": 9179,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.30C>T",
          "hgvs_p": "p.Ala10Ala"
        }
      ],
      "clinvar_disease": "6 conditions,Progressive sclerosing poliodystrophy",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2",
      "phenotype_combined": "Progressive sclerosing poliodystrophy|6 conditions",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}