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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: 16-31091334-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=31091334&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "16",
      "pos": 31091334,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_024006.6",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.292C>T",
          "hgvs_p": "p.Arg98Trp",
          "transcript": "NM_024006.6",
          "protein_id": "NP_076869.1",
          "transcript_support_level": null,
          "aa_start": 98,
          "aa_end": null,
          "aa_length": 163,
          "cds_start": 292,
          "cds_end": null,
          "cds_length": 492,
          "cdna_start": 360,
          "cdna_end": null,
          "cdna_length": 840,
          "mane_select": "ENST00000394975.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.292C>T",
          "hgvs_p": "p.Arg98Trp",
          "transcript": "ENST00000394975.3",
          "protein_id": "ENSP00000378426.2",
          "transcript_support_level": 1,
          "aa_start": 98,
          "aa_end": null,
          "aa_length": 163,
          "cds_start": 292,
          "cds_end": null,
          "cds_length": 492,
          "cdna_start": 360,
          "cdna_end": null,
          "cdna_length": 840,
          "mane_select": "NM_024006.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.374C>T",
          "hgvs_p": "p.Ala125Val",
          "transcript": "ENST00000319788.11",
          "protein_id": "ENSP00000326135.7",
          "transcript_support_level": 1,
          "aa_start": 125,
          "aa_end": null,
          "aa_length": 156,
          "cds_start": 374,
          "cds_end": null,
          "cds_length": 471,
          "cdna_start": 585,
          "cdna_end": null,
          "cdna_length": 1077,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.182C>T",
          "hgvs_p": "p.Ala61Val",
          "transcript": "ENST00000354895.4",
          "protein_id": "ENSP00000346969.4",
          "transcript_support_level": 1,
          "aa_start": 61,
          "aa_end": null,
          "aa_length": 92,
          "cds_start": 182,
          "cds_end": null,
          "cds_length": 279,
          "cdna_start": 409,
          "cdna_end": null,
          "cdna_length": 901,
          "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": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000255439",
          "gene_hgnc_id": null,
          "hgvs_c": "n.163C>T",
          "hgvs_p": null,
          "transcript": "ENST00000533518.5",
          "protein_id": "ENSP00000433035.1",
          "transcript_support_level": 1,
          "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": 2362,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000255439",
          "gene_hgnc_id": null,
          "hgvs_c": "c.283+1978C>T",
          "hgvs_p": null,
          "transcript": "ENST00000529564.1",
          "protein_id": "ENSP00000431371.1",
          "transcript_support_level": 4,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 165,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 498,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 725,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "W",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.376C>T",
          "hgvs_p": "p.Arg126Trp",
          "transcript": "NM_001311311.2",
          "protein_id": "NP_001298240.1",
          "transcript_support_level": null,
          "aa_start": 126,
          "aa_end": null,
          "aa_length": 191,
          "cds_start": 376,
          "cds_end": null,
          "cds_length": 576,
          "cdna_start": 444,
          "cdna_end": null,
          "cdna_length": 924,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.389C>T",
          "hgvs_p": "p.Ala130Val",
          "transcript": "ENST00000498155.1",
          "protein_id": "ENSP00000417662.1",
          "transcript_support_level": 5,
          "aa_start": 130,
          "aa_end": null,
          "aa_length": 161,
          "cds_start": 389,
          "cds_end": null,
          "cds_length": 486,
          "cdna_start": 711,
          "cdna_end": null,
          "cdna_length": 870,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.386C>T",
          "hgvs_p": "p.Ala129Val",
          "transcript": "ENST00000394971.7",
          "protein_id": "ENSP00000378422.3",
          "transcript_support_level": 5,
          "aa_start": 129,
          "aa_end": null,
          "aa_length": 160,
          "cds_start": 386,
          "cds_end": null,
          "cds_length": 483,
          "cdna_start": 434,
          "cdna_end": null,
          "cdna_length": 664,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.353C>T",
          "hgvs_p": "p.Ala118Val",
          "transcript": "ENST00000300851.10",
          "protein_id": "ENSP00000300851.6",
          "transcript_support_level": 2,
          "aa_start": 118,
          "aa_end": null,
          "aa_length": 149,
          "cds_start": 353,
          "cds_end": null,
          "cds_length": 450,
          "cdna_start": 384,
          "cdna_end": null,
          "cdna_length": 876,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "V",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.182C>T",
          "hgvs_p": "p.Ala61Val",
          "transcript": "NM_206824.3",
          "protein_id": "NP_996560.1",
          "transcript_support_level": null,
          "aa_start": 61,
          "aa_end": null,
          "aa_length": 92,
          "cds_start": 182,
          "cds_end": null,
          "cds_length": 279,
          "cdna_start": 250,
          "cdna_end": null,
          "cdna_length": 730,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "C",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.252C>T",
          "hgvs_p": "p.Cys84Cys",
          "transcript": "ENST00000420057.2",
          "protein_id": "ENSP00000437064.1",
          "transcript_support_level": 2,
          "aa_start": 84,
          "aa_end": null,
          "aa_length": 91,
          "cds_start": 252,
          "cds_end": null,
          "cds_length": 276,
          "cdna_start": 254,
          "cdna_end": null,
          "cdna_length": 746,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "5_prime_UTR_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VKORC1",
          "gene_hgnc_id": 23663,
          "hgvs_c": "c.-24C>T",
          "hgvs_p": null,
          "transcript": "ENST00000472468.1",
          "protein_id": "ENSP00000458994.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 42,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 129,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 461,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000255439",
          "gene_hgnc_id": null,
          "hgvs_c": "c.173+3223C>T",
          "hgvs_p": null,
          "transcript": "ENST00000532364.1",
          "protein_id": "ENSP00000460316.1",
          "transcript_support_level": 4,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 103,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 312,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 499,
          "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": "ENSG00000297437",
          "gene_hgnc_id": null,
          "hgvs_c": "n.164+314G>A",
          "hgvs_p": null,
          "transcript": "ENST00000747910.1",
          "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": 352,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "VKORC1",
      "gene_hgnc_id": 23663,
      "dbsnp": "rs72547528",
      "frequency_reference_population": 0.000058264366,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 94,
      "gnomad_exomes_af": 0.0000629655,
      "gnomad_genomes_af": 0.0000131391,
      "gnomad_exomes_ac": 92,
      "gnomad_genomes_ac": 2,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.5081248879432678,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.613,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.0982,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.17,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 0.653,
      "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": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM1,PM2,PP5_Moderate",
      "acmg_by_gene": [
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM1",
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_024006.6",
          "gene_symbol": "VKORC1",
          "hgnc_id": 23663,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,Unknown",
          "hgvs_c": "c.292C>T",
          "hgvs_p": "p.Arg98Trp"
        },
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000529564.1",
          "gene_symbol": "ENSG00000255439",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.283+1978C>T",
          "hgvs_p": null
        },
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000747910.1",
          "gene_symbol": "ENSG00000297437",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.164+314G>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " combined deficiency of, type 2,Hereditary combined deficiency of vitamin K-dependent clotting factors,Vitamin K-dependent clotting factors",
      "clinvar_classification": "Likely pathogenic",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LP:1",
      "phenotype_combined": "Vitamin K-dependent clotting factors, combined deficiency of, type 2|Hereditary combined deficiency of vitamin K-dependent clotting factors",
      "pathogenicity_classification_combined": "Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}