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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: 7-92494537-C-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=92494537&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "7",
      "pos": 92494537,
      "ref": "C",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000248633.9",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "c.2876G>C",
          "hgvs_p": "p.Arg959Pro",
          "transcript": "NM_000466.3",
          "protein_id": "NP_000457.1",
          "transcript_support_level": null,
          "aa_start": 959,
          "aa_end": null,
          "aa_length": 1283,
          "cds_start": 2876,
          "cds_end": null,
          "cds_length": 3852,
          "cdna_start": 2961,
          "cdna_end": null,
          "cdna_length": 4369,
          "mane_select": "ENST00000248633.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "c.2876G>C",
          "hgvs_p": "p.Arg959Pro",
          "transcript": "ENST00000248633.9",
          "protein_id": "ENSP00000248633.4",
          "transcript_support_level": 1,
          "aa_start": 959,
          "aa_end": null,
          "aa_length": 1283,
          "cds_start": 2876,
          "cds_end": null,
          "cds_length": 3852,
          "cdna_start": 2961,
          "cdna_end": null,
          "cdna_length": 4369,
          "mane_select": "NM_000466.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "c.2705G>C",
          "hgvs_p": "p.Arg902Pro",
          "transcript": "ENST00000428214.5",
          "protein_id": "ENSP00000394413.1",
          "transcript_support_level": 1,
          "aa_start": 902,
          "aa_end": null,
          "aa_length": 1226,
          "cds_start": 2705,
          "cds_end": null,
          "cds_length": 3681,
          "cdna_start": 2705,
          "cdna_end": null,
          "cdna_length": 3681,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 17,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "c.2705G>C",
          "hgvs_p": "p.Arg902Pro",
          "transcript": "NM_001282677.2",
          "protein_id": "NP_001269606.1",
          "transcript_support_level": null,
          "aa_start": 902,
          "aa_end": null,
          "aa_length": 1226,
          "cds_start": 2705,
          "cds_end": null,
          "cds_length": 3681,
          "cdna_start": 2790,
          "cdna_end": null,
          "cdna_length": 4198,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "c.2252G>C",
          "hgvs_p": "p.Arg751Pro",
          "transcript": "NM_001282678.2",
          "protein_id": "NP_001269607.1",
          "transcript_support_level": null,
          "aa_start": 751,
          "aa_end": null,
          "aa_length": 1075,
          "cds_start": 2252,
          "cds_end": null,
          "cds_length": 3228,
          "cdna_start": 2996,
          "cdna_end": null,
          "cdna_length": 4404,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "c.1910G>C",
          "hgvs_p": "p.Arg637Pro",
          "transcript": "ENST00000438045.5",
          "protein_id": "ENSP00000410438.1",
          "transcript_support_level": 2,
          "aa_start": 637,
          "aa_end": null,
          "aa_length": 961,
          "cds_start": 1910,
          "cds_end": null,
          "cds_length": 2886,
          "cdna_start": 1916,
          "cdna_end": null,
          "cdna_length": 3329,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 18,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "c.2876G>C",
          "hgvs_p": "p.Arg959Pro",
          "transcript": "XM_047420472.1",
          "protein_id": "XP_047276428.1",
          "transcript_support_level": null,
          "aa_start": 959,
          "aa_end": null,
          "aa_length": 1227,
          "cds_start": 2876,
          "cds_end": null,
          "cds_length": 3684,
          "cdna_start": 2961,
          "cdna_end": null,
          "cdna_length": 3846,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "c.1127G>C",
          "hgvs_p": "p.Arg376Pro",
          "transcript": "XM_047420473.1",
          "protein_id": "XP_047276429.1",
          "transcript_support_level": null,
          "aa_start": 376,
          "aa_end": null,
          "aa_length": 700,
          "cds_start": 1127,
          "cds_end": null,
          "cds_length": 2103,
          "cdna_start": 1295,
          "cdna_end": null,
          "cdna_length": 2703,
          "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": 18,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "n.2915G>C",
          "hgvs_p": null,
          "transcript": "ENST00000484913.5",
          "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": 4051,
          "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": 7,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PEX1",
          "gene_hgnc_id": 8850,
          "hgvs_c": "n.2768G>C",
          "hgvs_p": null,
          "transcript": "ENST00000496420.5",
          "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": 5333,
          "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": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000244055",
          "gene_hgnc_id": null,
          "hgvs_c": "n.3869C>G",
          "hgvs_p": null,
          "transcript": "ENST00000658444.1",
          "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": 4933,
          "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": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GATAD1",
          "gene_hgnc_id": 29941,
          "hgvs_c": "n.4323C>G",
          "hgvs_p": null,
          "transcript": "XR_927494.4",
          "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": 5555,
          "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": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "GATAD1",
          "gene_hgnc_id": 29941,
          "hgvs_c": "n.4254C>G",
          "hgvs_p": null,
          "transcript": "XR_927503.4",
          "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": 5486,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000244055",
          "gene_hgnc_id": null,
          "hgvs_c": "n.153+16718C>G",
          "hgvs_p": null,
          "transcript": "ENST00000746412.1",
          "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": 389,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PEX1",
      "gene_hgnc_id": 8850,
      "dbsnp": "rs773206107",
      "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": 0.9815495014190674,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.98,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9981,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.52,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 7.902,
      "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": 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": "ENST00000248633.9",
          "gene_symbol": "PEX1",
          "hgnc_id": 8850,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.2876G>C",
          "hgvs_p": "p.Arg959Pro"
        },
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000658444.1",
          "gene_symbol": "ENSG00000244055",
          "hgnc_id": null,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.3869C>G",
          "hgvs_p": null
        },
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "XR_927494.4",
          "gene_symbol": "GATAD1",
          "hgnc_id": 29941,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "n.4323C>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Heimler syndrome 1,Peroxisome biogenesis disorder 1A (Zellweger),Peroxisome biogenesis disorder 1B",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:3",
      "phenotype_combined": "Peroxisome biogenesis disorder 1A (Zellweger)|Peroxisome biogenesis disorder 1B|Heimler syndrome 1",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}