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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: 17-28725329-C-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=28725329&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "17",
      "pos": 28725329,
      "ref": "C",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "NM_138463.4",
      "consequences": [
        {
          "aa_ref": "W",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TLCD1",
          "gene_hgnc_id": 25177,
          "hgvs_c": "c.335G>C",
          "hgvs_p": "p.Trp112Ser",
          "transcript": "NM_138463.4",
          "protein_id": "NP_612472.1",
          "transcript_support_level": null,
          "aa_start": 112,
          "aa_end": null,
          "aa_length": 247,
          "cds_start": 335,
          "cds_end": null,
          "cds_length": 744,
          "cdna_start": 471,
          "cdna_end": null,
          "cdna_length": 1042,
          "mane_select": "ENST00000292090.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TLCD1",
          "gene_hgnc_id": 25177,
          "hgvs_c": "c.335G>C",
          "hgvs_p": "p.Trp112Ser",
          "transcript": "ENST00000292090.8",
          "protein_id": "ENSP00000292090.3",
          "transcript_support_level": 1,
          "aa_start": 112,
          "aa_end": null,
          "aa_length": 247,
          "cds_start": 335,
          "cds_end": null,
          "cds_length": 744,
          "cdna_start": 471,
          "cdna_end": null,
          "cdna_length": 1042,
          "mane_select": "NM_138463.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TLCD1",
          "gene_hgnc_id": 25177,
          "hgvs_c": "c.194G>C",
          "hgvs_p": "p.Trp65Ser",
          "transcript": "NM_001160407.2",
          "protein_id": "NP_001153879.1",
          "transcript_support_level": null,
          "aa_start": 65,
          "aa_end": null,
          "aa_length": 200,
          "cds_start": 194,
          "cds_end": null,
          "cds_length": 603,
          "cdna_start": 318,
          "cdna_end": null,
          "cdna_length": 889,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TLCD1",
          "gene_hgnc_id": 25177,
          "hgvs_c": "c.194G>C",
          "hgvs_p": "p.Trp65Ser",
          "transcript": "ENST00000394933.7",
          "protein_id": "ENSP00000378391.3",
          "transcript_support_level": 2,
          "aa_start": 65,
          "aa_end": null,
          "aa_length": 200,
          "cds_start": 194,
          "cds_end": null,
          "cds_length": 603,
          "cdna_start": 318,
          "cdna_end": null,
          "cdna_length": 784,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TLCD1",
          "gene_hgnc_id": 25177,
          "hgvs_c": "c.122G>C",
          "hgvs_p": "p.Trp41Ser",
          "transcript": "ENST00000580518.1",
          "protein_id": "ENSP00000466264.1",
          "transcript_support_level": 3,
          "aa_start": 41,
          "aa_end": null,
          "aa_length": 146,
          "cds_start": 122,
          "cds_end": null,
          "cds_length": 442,
          "cdna_start": 258,
          "cdna_end": null,
          "cdna_length": 578,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TLCD1",
          "gene_hgnc_id": 25177,
          "hgvs_c": "c.335G>C",
          "hgvs_p": "p.Trp112Ser",
          "transcript": "XM_011524278.4",
          "protein_id": "XP_011522580.1",
          "transcript_support_level": null,
          "aa_start": 112,
          "aa_end": null,
          "aa_length": 187,
          "cds_start": 335,
          "cds_end": null,
          "cds_length": 564,
          "cdna_start": 471,
          "cdna_end": null,
          "cdna_length": 957,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TLCD1",
          "gene_hgnc_id": 25177,
          "hgvs_c": "c.122G>C",
          "hgvs_p": "p.Trp41Ser",
          "transcript": "XM_006721671.5",
          "protein_id": "XP_006721734.1",
          "transcript_support_level": null,
          "aa_start": 41,
          "aa_end": null,
          "aa_length": 176,
          "cds_start": 122,
          "cds_end": null,
          "cds_length": 531,
          "cdna_start": 260,
          "cdna_end": null,
          "cdna_length": 831,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TLCD1",
          "gene_hgnc_id": 25177,
          "hgvs_c": "c.194G>C",
          "hgvs_p": "p.Trp65Ser",
          "transcript": "XM_047435299.1",
          "protein_id": "XP_047291255.1",
          "transcript_support_level": null,
          "aa_start": 65,
          "aa_end": null,
          "aa_length": 140,
          "cds_start": 194,
          "cds_end": null,
          "cds_length": 423,
          "cdna_start": 318,
          "cdna_end": null,
          "cdna_length": 804,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "TLCD1",
      "gene_hgnc_id": 25177,
      "dbsnp": null,
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9531451463699341,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.805,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.7613,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.37,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 6.697,
      "phylop100way_prediction": "Uncertain_significance",
      "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": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM2,PP3_Strong",
      "acmg_by_gene": [
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_138463.4",
          "gene_symbol": "TLCD1",
          "hgnc_id": 25177,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.335G>C",
          "hgvs_p": "p.Trp112Ser"
        }
      ],
      "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
}