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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: 16-2091144-C-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2091144&ref=C&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "16",
      "pos": 2091144,
      "ref": "C",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000262304.9",
      "consequences": [
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 43,
          "exon_rank_end": null,
          "exon_count": 46,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11743G>C",
          "hgvs_p": "p.Ala3915Pro",
          "transcript": "NM_001009944.3",
          "protein_id": "NP_001009944.3",
          "transcript_support_level": null,
          "aa_start": 3915,
          "aa_end": null,
          "aa_length": 4303,
          "cds_start": 11743,
          "cds_end": null,
          "cds_length": 12912,
          "cdna_start": 11952,
          "cdna_end": null,
          "cdna_length": 14140,
          "mane_select": "ENST00000262304.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 43,
          "exon_rank_end": null,
          "exon_count": 46,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11743G>C",
          "hgvs_p": "p.Ala3915Pro",
          "transcript": "ENST00000262304.9",
          "protein_id": "ENSP00000262304.4",
          "transcript_support_level": 1,
          "aa_start": 3915,
          "aa_end": null,
          "aa_length": 4303,
          "cds_start": 11743,
          "cds_end": null,
          "cds_length": 12912,
          "cdna_start": 11952,
          "cdna_end": null,
          "cdna_length": 14140,
          "mane_select": "NM_001009944.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 43,
          "exon_rank_end": null,
          "exon_count": 46,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11740G>C",
          "hgvs_p": "p.Ala3914Pro",
          "transcript": "ENST00000423118.5",
          "protein_id": "ENSP00000399501.1",
          "transcript_support_level": 1,
          "aa_start": 3914,
          "aa_end": null,
          "aa_length": 4302,
          "cds_start": 11740,
          "cds_end": null,
          "cds_length": 12909,
          "cdna_start": 11949,
          "cdna_end": null,
          "cdna_length": 14135,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 43,
          "exon_rank_end": null,
          "exon_count": 46,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11740G>C",
          "hgvs_p": "p.Ala3914Pro",
          "transcript": "NM_000296.4",
          "protein_id": "NP_000287.4",
          "transcript_support_level": null,
          "aa_start": 3914,
          "aa_end": null,
          "aa_length": 4302,
          "cds_start": 11740,
          "cds_end": null,
          "cds_length": 12909,
          "cdna_start": 11949,
          "cdna_end": null,
          "cdna_length": 14137,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 45,
          "exon_rank_end": null,
          "exon_count": 48,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11878G>C",
          "hgvs_p": "p.Ala3960Pro",
          "transcript": "XM_047434208.1",
          "protein_id": "XP_047290164.1",
          "transcript_support_level": null,
          "aa_start": 3960,
          "aa_end": null,
          "aa_length": 4348,
          "cds_start": 11878,
          "cds_end": null,
          "cds_length": 13047,
          "cdna_start": 12087,
          "cdna_end": null,
          "cdna_length": 14275,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 44,
          "exon_rank_end": null,
          "exon_count": 47,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11806G>C",
          "hgvs_p": "p.Ala3936Pro",
          "transcript": "XM_047434209.1",
          "protein_id": "XP_047290165.1",
          "transcript_support_level": null,
          "aa_start": 3936,
          "aa_end": null,
          "aa_length": 4324,
          "cds_start": 11806,
          "cds_end": null,
          "cds_length": 12975,
          "cdna_start": 12015,
          "cdna_end": null,
          "cdna_length": 14203,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 44,
          "exon_rank_end": null,
          "exon_count": 47,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11797G>C",
          "hgvs_p": "p.Ala3933Pro",
          "transcript": "XM_011522528.4",
          "protein_id": "XP_011520830.1",
          "transcript_support_level": null,
          "aa_start": 3933,
          "aa_end": null,
          "aa_length": 4321,
          "cds_start": 11797,
          "cds_end": null,
          "cds_length": 12966,
          "cdna_start": 11986,
          "cdna_end": null,
          "cdna_length": 14174,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 44,
          "exon_rank_end": null,
          "exon_count": 47,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11794G>C",
          "hgvs_p": "p.Ala3932Pro",
          "transcript": "XM_011522529.3",
          "protein_id": "XP_011520831.1",
          "transcript_support_level": null,
          "aa_start": 3932,
          "aa_end": null,
          "aa_length": 4320,
          "cds_start": 11794,
          "cds_end": null,
          "cds_length": 12963,
          "cdna_start": 11983,
          "cdna_end": null,
          "cdna_length": 14171,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 45,
          "exon_rank_end": null,
          "exon_count": 48,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11725G>C",
          "hgvs_p": "p.Ala3909Pro",
          "transcript": "XM_047434210.1",
          "protein_id": "XP_047290166.1",
          "transcript_support_level": null,
          "aa_start": 3909,
          "aa_end": null,
          "aa_length": 4297,
          "cds_start": 11725,
          "cds_end": null,
          "cds_length": 12894,
          "cdna_start": 12983,
          "cdna_end": null,
          "cdna_length": 15171,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 45,
          "exon_rank_end": null,
          "exon_count": 48,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.11668G>C",
          "hgvs_p": "p.Ala3890Pro",
          "transcript": "XM_047434211.1",
          "protein_id": "XP_047290167.1",
          "transcript_support_level": null,
          "aa_start": 3890,
          "aa_end": null,
          "aa_length": 4278,
          "cds_start": 11668,
          "cds_end": null,
          "cds_length": 12837,
          "cdna_start": 11887,
          "cdna_end": null,
          "cdna_length": 14075,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 36,
          "exon_rank_end": null,
          "exon_count": 39,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.9838G>C",
          "hgvs_p": "p.Ala3280Pro",
          "transcript": "XM_047434212.1",
          "protein_id": "XP_047290168.1",
          "transcript_support_level": null,
          "aa_start": 3280,
          "aa_end": null,
          "aa_length": 3668,
          "cds_start": 9838,
          "cds_end": null,
          "cds_length": 11007,
          "cdna_start": 9939,
          "cdna_end": null,
          "cdna_length": 12127,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 33,
          "exon_rank_end": null,
          "exon_count": 36,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.8821G>C",
          "hgvs_p": "p.Ala2941Pro",
          "transcript": "XM_011522537.2",
          "protein_id": "XP_011520839.1",
          "transcript_support_level": null,
          "aa_start": 2941,
          "aa_end": null,
          "aa_length": 3329,
          "cds_start": 8821,
          "cds_end": null,
          "cds_length": 9990,
          "cdna_start": 8910,
          "cdna_end": null,
          "cdna_length": 11098,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 33,
          "exon_rank_end": null,
          "exon_count": 36,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.8815G>C",
          "hgvs_p": "p.Ala2939Pro",
          "transcript": "XM_047434213.1",
          "protein_id": "XP_047290169.1",
          "transcript_support_level": null,
          "aa_start": 2939,
          "aa_end": null,
          "aa_length": 3327,
          "cds_start": 8815,
          "cds_end": null,
          "cds_length": 9984,
          "cdna_start": 8904,
          "cdna_end": null,
          "cdna_length": 11092,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 32,
          "exon_rank_end": null,
          "exon_count": 35,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "c.8698G>C",
          "hgvs_p": "p.Ala2900Pro",
          "transcript": "XM_005255370.4",
          "protein_id": "XP_005255427.1",
          "transcript_support_level": null,
          "aa_start": 2900,
          "aa_end": null,
          "aa_length": 3288,
          "cds_start": 8698,
          "cds_end": null,
          "cds_length": 9867,
          "cdna_start": 8870,
          "cdna_end": null,
          "cdna_length": 11058,
          "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": 30,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "n.*2936G>C",
          "hgvs_p": null,
          "transcript": "ENST00000487932.5",
          "protein_id": "ENSP00000457132.1",
          "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": 6464,
          "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": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "n.*267G>C",
          "hgvs_p": null,
          "transcript": "ENST00000561668.5",
          "protein_id": "ENSP00000461391.1",
          "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": 665,
          "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": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "n.264G>C",
          "hgvs_p": null,
          "transcript": "ENST00000564313.1",
          "protein_id": null,
          "transcript_support_level": 4,
          "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": 568,
          "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": 30,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "n.*2936G>C",
          "hgvs_p": null,
          "transcript": "ENST00000487932.5",
          "protein_id": "ENSP00000457132.1",
          "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": 6464,
          "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": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD1",
          "gene_hgnc_id": 9008,
          "hgvs_c": "n.*267G>C",
          "hgvs_p": null,
          "transcript": "ENST00000561668.5",
          "protein_id": "ENSP00000461391.1",
          "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": 665,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PKD1",
      "gene_hgnc_id": 9008,
      "dbsnp": "rs1555445237",
      "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": 0.8100593090057373,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.28,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.4789,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.41,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.116,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.01,
      "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": 5,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM1,PM2,PP3",
      "acmg_by_gene": [
        {
          "score": 5,
          "benign_score": 0,
          "pathogenic_score": 5,
          "criteria": [
            "PM1",
            "PM2",
            "PP3"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000262304.9",
          "gene_symbol": "PKD1",
          "hgnc_id": 9008,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.11743G>C",
          "hgvs_p": "p.Ala3915Pro"
        }
      ],
      "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
}