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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: 2-46581572-G-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=46581572&ref=G&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 46581572,
      "ref": "G",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_002643.4",
      "consequences": [
        {
          "aa_ref": "T",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "c.566C>G",
          "hgvs_p": "p.Thr189Arg",
          "transcript": "NM_002643.4",
          "protein_id": "NP_002634.1",
          "transcript_support_level": null,
          "aa_start": 189,
          "aa_end": null,
          "aa_length": 219,
          "cds_start": 566,
          "cds_end": null,
          "cds_length": 660,
          "cdna_start": 659,
          "cdna_end": null,
          "cdna_length": 1294,
          "mane_select": "ENST00000281382.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "c.566C>G",
          "hgvs_p": "p.Thr189Arg",
          "transcript": "ENST00000281382.11",
          "protein_id": "ENSP00000281382.6",
          "transcript_support_level": 1,
          "aa_start": 189,
          "aa_end": null,
          "aa_length": 219,
          "cds_start": 566,
          "cds_end": null,
          "cds_length": 660,
          "cdna_start": 659,
          "cdna_end": null,
          "cdna_length": 1294,
          "mane_select": "NM_002643.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RHOQ",
          "gene_hgnc_id": 17736,
          "hgvs_c": "c.*489G>C",
          "hgvs_p": null,
          "transcript": "NM_012249.4",
          "protein_id": "NP_036381.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 205,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 618,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4780,
          "mane_select": "ENST00000238738.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RHOQ",
          "gene_hgnc_id": 17736,
          "hgvs_c": "c.*489G>C",
          "hgvs_p": null,
          "transcript": "ENST00000238738.9",
          "protein_id": "ENSP00000238738.4",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 205,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 618,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4780,
          "mane_select": "NM_012249.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "c.*50C>G",
          "hgvs_p": null,
          "transcript": "ENST00000306465.8",
          "protein_id": "ENSP00000302663.4",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 206,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 621,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1061,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Y",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "c.618C>G",
          "hgvs_p": "p.Tyr206*",
          "transcript": "XM_011532908.4",
          "protein_id": "XP_011531210.1",
          "transcript_support_level": null,
          "aa_start": 206,
          "aa_end": null,
          "aa_length": 227,
          "cds_start": 618,
          "cds_end": null,
          "cds_length": 684,
          "cdna_start": 711,
          "cdna_end": null,
          "cdna_length": 1346,
          "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": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "n.*135C>G",
          "hgvs_p": null,
          "transcript": "ENST00000412717.1",
          "protein_id": "ENSP00000413202.1",
          "transcript_support_level": 3,
          "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": 737,
          "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": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "n.*125C>G",
          "hgvs_p": null,
          "transcript": "ENST00000420164.6",
          "protein_id": "ENSP00000410361.2",
          "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": 997,
          "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": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "n.568C>G",
          "hgvs_p": null,
          "transcript": "ENST00000482786.5",
          "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": 855,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "c.*50C>G",
          "hgvs_p": null,
          "transcript": "NM_173074.3",
          "protein_id": "NP_775097.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 206,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 621,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1399,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "n.*135C>G",
          "hgvs_p": null,
          "transcript": "ENST00000412717.1",
          "protein_id": "ENSP00000413202.1",
          "transcript_support_level": 3,
          "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": 737,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PIGF",
          "gene_hgnc_id": 8962,
          "hgvs_c": "n.*125C>G",
          "hgvs_p": null,
          "transcript": "ENST00000420164.6",
          "protein_id": "ENSP00000410361.2",
          "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": 997,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RHOQ",
          "gene_hgnc_id": 17736,
          "hgvs_c": "c.*644G>C",
          "hgvs_p": null,
          "transcript": "XM_011532726.3",
          "protein_id": "XP_011531028.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 192,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 579,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4896,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RHOQ",
          "gene_hgnc_id": 17736,
          "hgvs_c": "c.*489G>C",
          "hgvs_p": null,
          "transcript": "XM_005264229.3",
          "protein_id": "XP_005264286.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 118,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 357,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4519,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PIGF",
      "gene_hgnc_id": 8962,
      "dbsnp": "rs780985258",
      "frequency_reference_population": 0.0000037240434,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 6,
      "gnomad_exomes_af": 0.00000137082,
      "gnomad_genomes_af": 0.0000262864,
      "gnomad_exomes_ac": 2,
      "gnomad_genomes_ac": 4,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.7062398195266724,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.05000000074505806,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.303,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.8897,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.09,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 7.679,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0.05,
      "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": "Uncertain_significance",
      "acmg_criteria": "PM2",
      "acmg_by_gene": [
        {
          "score": 2,
          "benign_score": 0,
          "pathogenic_score": 2,
          "criteria": [
            "PM2"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_002643.4",
          "gene_symbol": "PIGF",
          "hgnc_id": 8962,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.566C>G",
          "hgvs_p": "p.Thr189Arg"
        },
        {
          "score": 2,
          "benign_score": 0,
          "pathogenic_score": 2,
          "criteria": [
            "PM2"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_012249.4",
          "gene_symbol": "RHOQ",
          "hgnc_id": 17736,
          "effects": [
            "3_prime_UTR_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.*489G>C",
          "hgvs_p": null
        }
      ],
      "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
}