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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: 2-120988904-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=120988904&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 120988904,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000361492.9",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2939C>T",
          "hgvs_p": "p.Pro980Leu",
          "transcript": "NM_001374353.1",
          "protein_id": "NP_001361282.1",
          "transcript_support_level": null,
          "aa_start": 980,
          "aa_end": null,
          "aa_length": 1569,
          "cds_start": 2939,
          "cds_end": null,
          "cds_length": 4710,
          "cdna_start": 3387,
          "cdna_end": null,
          "cdna_length": 7136,
          "mane_select": "ENST00000361492.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2939C>T",
          "hgvs_p": "p.Pro980Leu",
          "transcript": "ENST00000361492.9",
          "protein_id": "ENSP00000354586.5",
          "transcript_support_level": 1,
          "aa_start": 980,
          "aa_end": null,
          "aa_length": 1569,
          "cds_start": 2939,
          "cds_end": null,
          "cds_length": 4710,
          "cdna_start": 3387,
          "cdna_end": null,
          "cdna_length": 7136,
          "mane_select": "NM_001374353.1",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2990C>T",
          "hgvs_p": "p.Pro997Leu",
          "transcript": "NM_001371271.1",
          "protein_id": "NP_001358200.1",
          "transcript_support_level": null,
          "aa_start": 997,
          "aa_end": null,
          "aa_length": 1586,
          "cds_start": 2990,
          "cds_end": null,
          "cds_length": 4761,
          "cdna_start": 3438,
          "cdna_end": null,
          "cdna_length": 7187,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2990C>T",
          "hgvs_p": "p.Pro997Leu",
          "transcript": "NM_005270.5",
          "protein_id": "NP_005261.2",
          "transcript_support_level": null,
          "aa_start": 997,
          "aa_end": null,
          "aa_length": 1586,
          "cds_start": 2990,
          "cds_end": null,
          "cds_length": 4761,
          "cdna_start": 3178,
          "cdna_end": null,
          "cdna_length": 6927,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2990C>T",
          "hgvs_p": "p.Pro997Leu",
          "transcript": "ENST00000452319.6",
          "protein_id": "ENSP00000390436.1",
          "transcript_support_level": 5,
          "aa_start": 997,
          "aa_end": null,
          "aa_length": 1586,
          "cds_start": 2990,
          "cds_end": null,
          "cds_length": 4761,
          "cdna_start": 2990,
          "cdna_end": null,
          "cdna_length": 4761,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2564C>T",
          "hgvs_p": "p.Pro855Leu",
          "transcript": "NM_001374354.1",
          "protein_id": "NP_001361283.1",
          "transcript_support_level": null,
          "aa_start": 855,
          "aa_end": null,
          "aa_length": 1444,
          "cds_start": 2564,
          "cds_end": null,
          "cds_length": 4335,
          "cdna_start": 3281,
          "cdna_end": null,
          "cdna_length": 7030,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2972C>T",
          "hgvs_p": "p.Pro991Leu",
          "transcript": "XM_011510969.3",
          "protein_id": "XP_011509271.3",
          "transcript_support_level": null,
          "aa_start": 991,
          "aa_end": null,
          "aa_length": 1580,
          "cds_start": 2972,
          "cds_end": null,
          "cds_length": 4743,
          "cdna_start": 2981,
          "cdna_end": null,
          "cdna_length": 6730,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2939C>T",
          "hgvs_p": "p.Pro980Leu",
          "transcript": "XM_047443947.1",
          "protein_id": "XP_047299903.1",
          "transcript_support_level": null,
          "aa_start": 980,
          "aa_end": null,
          "aa_length": 1569,
          "cds_start": 2939,
          "cds_end": null,
          "cds_length": 4710,
          "cdna_start": 3127,
          "cdna_end": null,
          "cdna_length": 6876,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2921C>T",
          "hgvs_p": "p.Pro974Leu",
          "transcript": "XM_017003818.2",
          "protein_id": "XP_016859307.2",
          "transcript_support_level": null,
          "aa_start": 974,
          "aa_end": null,
          "aa_length": 1563,
          "cds_start": 2921,
          "cds_end": null,
          "cds_length": 4692,
          "cdna_start": 2930,
          "cdna_end": null,
          "cdna_length": 6679,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "c.2795C>T",
          "hgvs_p": "p.Pro932Leu",
          "transcript": "XM_011510971.3",
          "protein_id": "XP_011509273.1",
          "transcript_support_level": null,
          "aa_start": 932,
          "aa_end": null,
          "aa_length": 1521,
          "cds_start": 2795,
          "cds_end": null,
          "cds_length": 4566,
          "cdna_start": 2956,
          "cdna_end": null,
          "cdna_length": 6705,
          "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": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "n.*2038C>T",
          "hgvs_p": null,
          "transcript": "ENST00000341310.10",
          "protein_id": "ENSP00000344473.6",
          "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": 4904,
          "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": 10,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "n.*2089C>T",
          "hgvs_p": null,
          "transcript": "ENST00000438299.5",
          "protein_id": "ENSP00000400593.1",
          "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": 3724,
          "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": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "n.*2089C>T",
          "hgvs_p": null,
          "transcript": "ENST00000445186.5",
          "protein_id": "ENSP00000397488.1",
          "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": 4955,
          "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": 10,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "n.*2038C>T",
          "hgvs_p": null,
          "transcript": "ENST00000452692.5",
          "protein_id": "ENSP00000403715.1",
          "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": 3673,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "n.*2038C>T",
          "hgvs_p": null,
          "transcript": "ENST00000341310.10",
          "protein_id": "ENSP00000344473.6",
          "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": 4904,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "n.*2089C>T",
          "hgvs_p": null,
          "transcript": "ENST00000438299.5",
          "protein_id": "ENSP00000400593.1",
          "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": 3724,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "n.*2089C>T",
          "hgvs_p": null,
          "transcript": "ENST00000445186.5",
          "protein_id": "ENSP00000397488.1",
          "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": 4955,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GLI2",
          "gene_hgnc_id": 4318,
          "hgvs_c": "n.*2038C>T",
          "hgvs_p": null,
          "transcript": "ENST00000452692.5",
          "protein_id": "ENSP00000403715.1",
          "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": 3673,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "GLI2",
      "gene_hgnc_id": 4318,
      "dbsnp": "rs563818052",
      "frequency_reference_population": 0.000010597907,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 16,
      "gnomad_exomes_af": 0.0000110454,
      "gnomad_genomes_af": 0.00000659187,
      "gnomad_exomes_ac": 15,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.07029387354850769,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.007,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0673,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.74,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.757,
      "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": -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": "ENST00000361492.9",
          "gene_symbol": "GLI2",
          "hgnc_id": 4318,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.2939C>T",
          "hgvs_p": "p.Pro980Leu"
        }
      ],
      "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
}