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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: 1-244858217-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=244858217&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 244858217,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "ENST00000640218.2",
      "consequences": [
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.1288G>A",
          "hgvs_p": "p.Val430Ile",
          "transcript": "NM_031844.3",
          "protein_id": "NP_114032.2",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 825,
          "cds_start": 1288,
          "cds_end": null,
          "cds_length": 2478,
          "cdna_start": 1524,
          "cdna_end": null,
          "cdna_length": 6867,
          "mane_select": "ENST00000640218.2",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.1288G>A",
          "hgvs_p": "p.Val430Ile",
          "transcript": "ENST00000640218.2",
          "protein_id": "ENSP00000491215.1",
          "transcript_support_level": 1,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 825,
          "cds_start": 1288,
          "cds_end": null,
          "cds_length": 2478,
          "cdna_start": 1524,
          "cdna_end": null,
          "cdna_length": 6867,
          "mane_select": "NM_031844.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.1231G>A",
          "hgvs_p": "p.Val411Ile",
          "transcript": "ENST00000444376.7",
          "protein_id": "ENSP00000393151.2",
          "transcript_support_level": 1,
          "aa_start": 411,
          "aa_end": null,
          "aa_length": 806,
          "cds_start": 1231,
          "cds_end": null,
          "cds_length": 2421,
          "cdna_start": 1484,
          "cdna_end": null,
          "cdna_length": 6827,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.460G>A",
          "hgvs_p": "p.Val154Ile",
          "transcript": "ENST00000639628.2",
          "protein_id": "ENSP00000491340.1",
          "transcript_support_level": 1,
          "aa_start": 154,
          "aa_end": null,
          "aa_length": 549,
          "cds_start": 460,
          "cds_end": null,
          "cds_length": 1650,
          "cdna_start": 2331,
          "cdna_end": null,
          "cdna_length": 7674,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.1231G>A",
          "hgvs_p": "p.Val411Ile",
          "transcript": "NM_004501.3",
          "protein_id": "NP_004492.2",
          "transcript_support_level": null,
          "aa_start": 411,
          "aa_end": null,
          "aa_length": 806,
          "cds_start": 1231,
          "cds_end": null,
          "cds_length": 2421,
          "cdna_start": 1449,
          "cdna_end": null,
          "cdna_length": 6789,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.1045G>A",
          "hgvs_p": "p.Val349Ile",
          "transcript": "ENST00000283179.14",
          "protein_id": "ENSP00000283179.10",
          "transcript_support_level": 5,
          "aa_start": 349,
          "aa_end": null,
          "aa_length": 744,
          "cds_start": 1045,
          "cds_end": null,
          "cds_length": 2235,
          "cdna_start": 1232,
          "cdna_end": null,
          "cdna_length": 3120,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.997G>A",
          "hgvs_p": "p.Val333Ile",
          "transcript": "ENST00000638475.1",
          "protein_id": "ENSP00000491305.1",
          "transcript_support_level": 5,
          "aa_start": 333,
          "aa_end": null,
          "aa_length": 728,
          "cds_start": 997,
          "cds_end": null,
          "cds_length": 2187,
          "cdna_start": 997,
          "cdna_end": null,
          "cdna_length": 2698,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.907G>A",
          "hgvs_p": "p.Val303Ile",
          "transcript": "ENST00000704074.1",
          "protein_id": "ENSP00000515674.1",
          "transcript_support_level": null,
          "aa_start": 303,
          "aa_end": null,
          "aa_length": 664,
          "cds_start": 907,
          "cds_end": null,
          "cds_length": 1995,
          "cdna_start": 909,
          "cdna_end": null,
          "cdna_length": 3015,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.619G>A",
          "hgvs_p": "p.Val207Ile",
          "transcript": "ENST00000440865.2",
          "protein_id": "ENSP00000410728.2",
          "transcript_support_level": 2,
          "aa_start": 207,
          "aa_end": null,
          "aa_length": 602,
          "cds_start": 619,
          "cds_end": null,
          "cds_length": 1809,
          "cdna_start": 973,
          "cdna_end": null,
          "cdna_length": 3207,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.454G>A",
          "hgvs_p": "p.Val152Ile",
          "transcript": "ENST00000638716.1",
          "protein_id": "ENSP00000491601.1",
          "transcript_support_level": 5,
          "aa_start": 152,
          "aa_end": null,
          "aa_length": 547,
          "cds_start": 454,
          "cds_end": null,
          "cds_length": 1644,
          "cdna_start": 467,
          "cdna_end": null,
          "cdna_length": 2640,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.460G>A",
          "hgvs_p": "p.Val154Ile",
          "transcript": "ENST00000640001.1",
          "protein_id": "ENSP00000491294.1",
          "transcript_support_level": 5,
          "aa_start": 154,
          "aa_end": null,
          "aa_length": 546,
          "cds_start": 460,
          "cds_end": null,
          "cds_length": 1641,
          "cdna_start": 2318,
          "cdna_end": null,
          "cdna_length": 4227,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "V",
          "aa_alt": "I",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "c.271G>A",
          "hgvs_p": "p.Val91Ile",
          "transcript": "ENST00000483966.3",
          "protein_id": "ENSP00000492573.1",
          "transcript_support_level": 2,
          "aa_start": 91,
          "aa_end": null,
          "aa_length": 302,
          "cds_start": 271,
          "cds_end": null,
          "cds_length": 909,
          "cdna_start": 271,
          "cdna_end": null,
          "cdna_length": 1069,
          "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": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.901G>A",
          "hgvs_p": null,
          "transcript": "ENST00000366525.8",
          "protein_id": null,
          "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": 2851,
          "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": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.685G>A",
          "hgvs_p": null,
          "transcript": "ENST00000465881.2",
          "protein_id": null,
          "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": 883,
          "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": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.1348G>A",
          "hgvs_p": null,
          "transcript": "ENST00000468690.2",
          "protein_id": null,
          "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": 5273,
          "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": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.3402G>A",
          "hgvs_p": null,
          "transcript": "ENST00000476241.2",
          "protein_id": null,
          "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": 4844,
          "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": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.397G>A",
          "hgvs_p": null,
          "transcript": "ENST00000638230.1",
          "protein_id": "ENSP00000492010.1",
          "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": 1922,
          "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": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.460G>A",
          "hgvs_p": null,
          "transcript": "ENST00000638301.1",
          "protein_id": "ENSP00000491807.1",
          "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": 3650,
          "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": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.2056G>A",
          "hgvs_p": null,
          "transcript": "ENST00000638589.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2225,
          "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": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.3505G>A",
          "hgvs_p": null,
          "transcript": "ENST00000638952.1",
          "protein_id": null,
          "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": 5678,
          "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": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "HNRNPU",
          "gene_hgnc_id": 5048,
          "hgvs_c": "n.3278G>A",
          "hgvs_p": null,
          "transcript": "ENST00000639667.1",
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      ],
      "gene_symbol": "HNRNPU",
      "gene_hgnc_id": 5048,
      "dbsnp": "rs772732188",
      "frequency_reference_population": 0.000014872156,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 24,
      "gnomad_exomes_af": 0.0000157361,
      "gnomad_genomes_af": 0.00000657263,
      "gnomad_exomes_ac": 23,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.17145046591758728,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.307,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.0666,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.4,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.75,
      "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": -11,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Moderate,BP6,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -11,
          "benign_score": 11,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BP6",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000640218.2",
          "gene_symbol": "HNRNPU",
          "hgnc_id": 5048,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.1288G>A",
          "hgvs_p": "p.Val430Ile"
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      ],
      "clinvar_disease": " 54,Developmental and epileptic encephalopathy,Inborn genetic diseases,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:2 LB:1",
      "phenotype_combined": "Developmental and epileptic encephalopathy, 54|Inborn genetic diseases|not provided",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}