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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: 1-155238144-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=155238144&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 155238144,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000368373.8",
      "consequences": [
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.751T>C",
          "hgvs_p": "p.Tyr251His",
          "transcript": "NM_000157.4",
          "protein_id": "NP_000148.2",
          "transcript_support_level": null,
          "aa_start": 251,
          "aa_end": null,
          "aa_length": 536,
          "cds_start": 751,
          "cds_end": null,
          "cds_length": 1611,
          "cdna_start": 888,
          "cdna_end": null,
          "cdna_length": 2291,
          "mane_select": "ENST00000368373.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.751T>C",
          "hgvs_p": "p.Tyr251His",
          "transcript": "ENST00000368373.8",
          "protein_id": "ENSP00000357357.3",
          "transcript_support_level": 1,
          "aa_start": 251,
          "aa_end": null,
          "aa_length": 536,
          "cds_start": 751,
          "cds_end": null,
          "cds_length": 1611,
          "cdna_start": 888,
          "cdna_end": null,
          "cdna_length": 2291,
          "mane_select": "NM_000157.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.751T>C",
          "hgvs_p": "p.Tyr251His",
          "transcript": "ENST00000327247.9",
          "protein_id": "ENSP00000314508.5",
          "transcript_support_level": 1,
          "aa_start": 251,
          "aa_end": null,
          "aa_length": 536,
          "cds_start": 751,
          "cds_end": null,
          "cds_length": 1611,
          "cdna_start": 984,
          "cdna_end": null,
          "cdna_length": 2387,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.751T>C",
          "hgvs_p": "p.Tyr251His",
          "transcript": "NM_001005741.3",
          "protein_id": "NP_001005741.1",
          "transcript_support_level": null,
          "aa_start": 251,
          "aa_end": null,
          "aa_length": 536,
          "cds_start": 751,
          "cds_end": null,
          "cds_length": 1611,
          "cdna_start": 941,
          "cdna_end": null,
          "cdna_length": 2344,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.751T>C",
          "hgvs_p": "p.Tyr251His",
          "transcript": "NM_001005742.3",
          "protein_id": "NP_001005742.1",
          "transcript_support_level": null,
          "aa_start": 251,
          "aa_end": null,
          "aa_length": 536,
          "cds_start": 751,
          "cds_end": null,
          "cds_length": 1611,
          "cdna_start": 922,
          "cdna_end": null,
          "cdna_length": 2325,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.604T>C",
          "hgvs_p": "p.Tyr202His",
          "transcript": "NM_001171812.2",
          "protein_id": "NP_001165283.1",
          "transcript_support_level": null,
          "aa_start": 202,
          "aa_end": null,
          "aa_length": 487,
          "cds_start": 604,
          "cds_end": null,
          "cds_length": 1464,
          "cdna_start": 741,
          "cdna_end": null,
          "cdna_length": 2144,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.604T>C",
          "hgvs_p": "p.Tyr202His",
          "transcript": "ENST00000427500.7",
          "protein_id": "ENSP00000402577.2",
          "transcript_support_level": 2,
          "aa_start": 202,
          "aa_end": null,
          "aa_length": 487,
          "cds_start": 604,
          "cds_end": null,
          "cds_length": 1464,
          "cdna_start": 767,
          "cdna_end": null,
          "cdna_length": 2063,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.490T>C",
          "hgvs_p": "p.Tyr164His",
          "transcript": "NM_001171811.2",
          "protein_id": "NP_001165282.1",
          "transcript_support_level": null,
          "aa_start": 164,
          "aa_end": null,
          "aa_length": 449,
          "cds_start": 490,
          "cds_end": null,
          "cds_length": 1350,
          "cdna_start": 758,
          "cdna_end": null,
          "cdna_length": 2161,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "c.490T>C",
          "hgvs_p": "p.Tyr164His",
          "transcript": "ENST00000428024.3",
          "protein_id": "ENSP00000397986.2",
          "transcript_support_level": 2,
          "aa_start": 164,
          "aa_end": null,
          "aa_length": 449,
          "cds_start": 490,
          "cds_end": null,
          "cds_length": 1350,
          "cdna_start": 830,
          "cdna_end": null,
          "cdna_length": 1817,
          "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": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "n.538T>C",
          "hgvs_p": null,
          "transcript": "ENST00000460156.1",
          "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": 750,
          "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": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "n.356T>C",
          "hgvs_p": null,
          "transcript": "ENST00000491081.5",
          "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": 892,
          "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": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "n.374T>C",
          "hgvs_p": null,
          "transcript": "ENST00000497670.5",
          "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": 696,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "n.339+1829T>C",
          "hgvs_p": null,
          "transcript": "ENST00000484489.5",
          "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": 749,
          "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": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GBA1",
          "gene_hgnc_id": 4177,
          "hgvs_c": "n.*69T>C",
          "hgvs_p": null,
          "transcript": "ENST00000493842.5",
          "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": 1020,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "GBA1",
      "gene_hgnc_id": 4177,
      "dbsnp": "rs121908300",
      "frequency_reference_population": 0.0000013681014,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": 0.0000013681,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 2,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9861769080162048,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.928,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9243,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.54,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 8.099,
      "phylop100way_prediction": "Pathogenic",
      "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": 9,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM1,PM2,PP2,PP3_Strong",
      "acmg_by_gene": [
        {
          "score": 9,
          "benign_score": 0,
          "pathogenic_score": 9,
          "criteria": [
            "PM1",
            "PM2",
            "PP2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000368373.8",
          "gene_symbol": "GBA1",
          "hgnc_id": 4177,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.751T>C",
          "hgvs_p": "p.Tyr251His"
        }
      ],
      "clinvar_disease": "Gaucher disease,Gaucher disease type I,not provided",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "US:2",
      "phenotype_combined": "Gaucher disease type I|Gaucher disease|not provided",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}