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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: 2-58159419-A-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=58159419&ref=A&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 58159419,
      "ref": "A",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_006296.7",
      "consequences": [
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro",
          "transcript": "NM_006296.7",
          "protein_id": "NP_006287.2",
          "transcript_support_level": null,
          "aa_start": 418,
          "aa_end": null,
          "aa_length": 508,
          "cds_start": 1253,
          "cds_end": null,
          "cds_length": 1527,
          "cdna_start": 1321,
          "cdna_end": null,
          "cdna_length": 1773,
          "mane_select": "ENST00000340157.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro",
          "transcript": "ENST00000340157.9",
          "protein_id": "ENSP00000342381.4",
          "transcript_support_level": 1,
          "aa_start": 418,
          "aa_end": null,
          "aa_length": 508,
          "cds_start": 1253,
          "cds_end": null,
          "cds_length": 1527,
          "cdna_start": 1321,
          "cdna_end": null,
          "cdna_length": 1773,
          "mane_select": "NM_006296.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro",
          "transcript": "ENST00000435505.6",
          "protein_id": "ENSP00000408002.2",
          "transcript_support_level": 1,
          "aa_start": 418,
          "aa_end": null,
          "aa_length": 508,
          "cds_start": 1253,
          "cds_end": null,
          "cds_length": 1527,
          "cdna_start": 1998,
          "cdna_end": null,
          "cdna_length": 2446,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1184A>C",
          "hgvs_p": "p.Gln395Pro",
          "transcript": "ENST00000440705.6",
          "protein_id": "ENSP00000398323.2",
          "transcript_support_level": 1,
          "aa_start": 395,
          "aa_end": null,
          "aa_length": 485,
          "cds_start": 1184,
          "cds_end": null,
          "cds_length": 1458,
          "cdna_start": 1311,
          "cdna_end": null,
          "cdna_length": 1676,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.899A>C",
          "hgvs_p": "p.Gln300Pro",
          "transcript": "ENST00000412104.6",
          "protein_id": "ENSP00000404156.3",
          "transcript_support_level": 1,
          "aa_start": 300,
          "aa_end": null,
          "aa_length": 390,
          "cds_start": 899,
          "cds_end": null,
          "cds_length": 1173,
          "cdna_start": 1415,
          "cdna_end": null,
          "cdna_length": 1916,
          "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": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "n.*1210A>C",
          "hgvs_p": null,
          "transcript": "ENST00000432057.2",
          "protein_id": "ENSP00000400006.1",
          "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": 1870,
          "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": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FANCL",
          "gene_hgnc_id": 20748,
          "hgvs_c": "c.*346T>G",
          "hgvs_p": null,
          "transcript": "NM_018062.4",
          "protein_id": "NP_060532.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 375,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 1128,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1658,
          "mane_select": "ENST00000233741.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FANCL",
          "gene_hgnc_id": 20748,
          "hgvs_c": "c.*346T>G",
          "hgvs_p": null,
          "transcript": "ENST00000233741.9",
          "protein_id": "ENSP00000233741.5",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 375,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 1128,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1658,
          "mane_select": "NM_018062.4",
          "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": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FANCL",
          "gene_hgnc_id": 20748,
          "hgvs_c": "c.*346T>G",
          "hgvs_p": null,
          "transcript": "ENST00000403295.8",
          "protein_id": "ENSP00000386097.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 347,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 1044,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1598,
          "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": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FANCL",
          "gene_hgnc_id": 20748,
          "hgvs_c": "c.*346T>G",
          "hgvs_p": null,
          "transcript": "ENST00000449070.6",
          "protein_id": "ENSP00000401280.2",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 316,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 951,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1526,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "n.*1210A>C",
          "hgvs_p": null,
          "transcript": "ENST00000432057.2",
          "protein_id": "ENSP00000400006.1",
          "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": 1870,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro",
          "transcript": "NM_001130480.2",
          "protein_id": "NP_001123952.1",
          "transcript_support_level": null,
          "aa_start": 418,
          "aa_end": null,
          "aa_length": 508,
          "cds_start": 1253,
          "cds_end": null,
          "cds_length": 1527,
          "cdna_start": 1438,
          "cdna_end": null,
          "cdna_length": 1939,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro",
          "transcript": "NM_001130481.2",
          "protein_id": "NP_001123953.1",
          "transcript_support_level": null,
          "aa_start": 418,
          "aa_end": null,
          "aa_length": 508,
          "cds_start": 1253,
          "cds_end": null,
          "cds_length": 1527,
          "cdna_start": 1280,
          "cdna_end": null,
          "cdna_length": 1781,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 16,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro",
          "transcript": "NM_001288837.2",
          "protein_id": "NP_001275766.1",
          "transcript_support_level": null,
          "aa_start": 418,
          "aa_end": null,
          "aa_length": 508,
          "cds_start": 1253,
          "cds_end": null,
          "cds_length": 1527,
          "cdna_start": 2057,
          "cdna_end": null,
          "cdna_length": 2509,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1184A>C",
          "hgvs_p": "p.Gln395Pro",
          "transcript": "NM_001130482.2",
          "protein_id": "NP_001123954.1",
          "transcript_support_level": null,
          "aa_start": 395,
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          "cds_start": 1184,
          "cds_end": null,
          "cds_length": 1458,
          "cdna_start": 1384,
          "cdna_end": null,
          "cdna_length": 1885,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.899A>C",
          "hgvs_p": "p.Gln300Pro",
          "transcript": "NM_001288836.1",
          "protein_id": "NP_001275765.1",
          "transcript_support_level": null,
          "aa_start": 300,
          "aa_end": null,
          "aa_length": 390,
          "cds_start": 899,
          "cds_end": null,
          "cds_length": 1173,
          "cdna_start": 1575,
          "cdna_end": null,
          "cdna_length": 2076,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.899A>C",
          "hgvs_p": "p.Gln300Pro",
          "transcript": "NM_001288839.2",
          "protein_id": "NP_001275768.1",
          "transcript_support_level": null,
          "aa_start": 300,
          "aa_end": null,
          "aa_length": 390,
          "cds_start": 899,
          "cds_end": null,
          "cds_length": 1173,
          "cdna_start": 1251,
          "cdna_end": null,
          "cdna_length": 1703,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro",
          "transcript": "XM_005264540.5",
          "protein_id": "XP_005264597.1",
          "transcript_support_level": null,
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          "aa_length": 508,
          "cds_start": 1253,
          "cds_end": null,
          "cds_length": 1527,
          "cdna_start": 1581,
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          "cdna_length": 2082,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro",
          "transcript": "XM_011533092.4",
          "protein_id": "XP_011531394.1",
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          "cds_start": 1253,
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          "cdna_start": 1440,
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          "cdna_length": 1941,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
          "hgvs_c": "c.899A>C",
          "hgvs_p": "p.Gln300Pro",
          "transcript": "XM_047445745.1",
          "protein_id": "XP_047301701.1",
          "transcript_support_level": null,
          "aa_start": 300,
          "aa_end": null,
          "aa_length": 390,
          "cds_start": 899,
          "cds_end": null,
          "cds_length": 1173,
          "cdna_start": 1093,
          "cdna_end": null,
          "cdna_length": 1594,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "Q",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "VRK2",
          "gene_hgnc_id": 12719,
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        {
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        }
      ],
      "gene_symbol": "VRK2",
      "gene_hgnc_id": 12719,
      "dbsnp": "rs778693777",
      "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": 0.1539253294467926,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.104,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.0729,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.46,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.336,
      "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": 0,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,BP4_Moderate",
      "acmg_by_gene": [
        {
          "score": 0,
          "benign_score": 2,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_006296.7",
          "gene_symbol": "VRK2",
          "hgnc_id": 12719,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1253A>C",
          "hgvs_p": "p.Gln418Pro"
        },
        {
          "score": 0,
          "benign_score": 2,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_018062.4",
          "gene_symbol": "FANCL",
          "hgnc_id": 20748,
          "effects": [
            "3_prime_UTR_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.*346T>G",
          "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
}