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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: 2-47403326-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=47403326&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 47403326,
      "ref": "G",
      "alt": "A",
      "effect": "synonymous_variant",
      "transcript": "NM_000251.3",
      "consequences": [
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_000251.3",
          "protein_id": "NP_000242.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 934,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2805,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 3115,
          "mane_select": "ENST00000233146.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "ENST00000233146.7",
          "protein_id": "ENSP00000233146.2",
          "transcript_support_level": 1,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 934,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2805,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 3115,
          "mane_select": "NM_000251.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "ENST00000406134.5",
          "protein_id": "ENSP00000384199.1",
          "transcript_support_level": 1,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 921,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2766,
          "cdna_start": 197,
          "cdna_end": null,
          "cdna_length": 3628,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406674.1",
          "protein_id": "NP_001393603.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 1014,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 3045,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 5813,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406631.1",
          "protein_id": "NP_001393560.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 979,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2940,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 3210,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406632.1",
          "protein_id": "NP_001393561.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 976,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2931,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 3284,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406633.1",
          "protein_id": "NP_001393562.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 975,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2928,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 3134,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406634.1",
          "protein_id": "NP_001393563.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 974,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2925,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 5693,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406635.1",
          "protein_id": "NP_001393564.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 969,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2910,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 3051,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406636.1",
          "protein_id": "NP_001393565.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 958,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2877,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 3018,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
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          "exon_count": 17,
          "intron_rank": null,
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          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406637.1",
          "protein_id": "NP_001393566.1",
          "transcript_support_level": null,
          "aa_start": 45,
          "aa_end": null,
          "aa_length": 957,
          "cds_start": 135,
          "cds_end": null,
          "cds_length": 2874,
          "cdna_start": 171,
          "cdna_end": null,
          "cdna_length": 4436,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
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          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406638.1",
          "protein_id": "NP_001393567.1",
          "transcript_support_level": null,
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          "cdna_start": 171,
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          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
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          "exon_count": 18,
          "intron_rank": null,
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          "gene_symbol": "MSH2",
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          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406639.1",
          "protein_id": "NP_001393568.1",
          "transcript_support_level": null,
          "aa_start": 45,
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          "mane_select": null,
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 1,
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          "intron_rank": null,
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          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406640.1",
          "protein_id": "NP_001393569.1",
          "transcript_support_level": null,
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          "cdna_start": 171,
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          "mane_select": null,
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        },
        {
          "aa_ref": "A",
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          ],
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          "gene_symbol": "MSH2",
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          "hgvs_p": "p.Ala45Ala",
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        },
        {
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          "strand": true,
          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406642.1",
          "protein_id": "NP_001393571.1",
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          "cdna_start": 171,
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          "mane_select": null,
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        {
          "aa_ref": "A",
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          "strand": true,
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          ],
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          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406643.1",
          "protein_id": "NP_001393572.1",
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        },
        {
          "aa_ref": "A",
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          "consequences": [
            "synonymous_variant"
          ],
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          "gene_symbol": "MSH2",
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        {
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          "strand": true,
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          ],
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          "exon_count": 17,
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          "gene_symbol": "MSH2",
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          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
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        },
        {
          "aa_ref": "A",
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          "consequences": [
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          ],
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          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
          "transcript": "NM_001406645.1",
          "protein_id": "NP_001393574.1",
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          "cdna_start": 171,
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          "cdna_length": 10404,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
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          "exon_count": 17,
          "intron_rank": null,
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          "gene_symbol": "MSH2",
          "gene_hgnc_id": 7325,
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala",
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          "protein_id": "NP_001245210.1",
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        {
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          "gene_symbol": "MSH2",
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          "transcript": "ENST00000543555.6",
          "protein_id": "ENSP00000442697.1",
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        }
      ],
      "gene_symbol": "MSH2",
      "gene_hgnc_id": 7325,
      "dbsnp": "rs890172773",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": 0,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 0,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.49000000953674316,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.49,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.649,
      "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": "PM2,BP4_Strong,BP6_Very_Strong,BP7",
      "acmg_by_gene": [
        {
          "score": -11,
          "benign_score": 13,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7"
          ],
          "verdict": "Benign",
          "transcript": "NM_000251.3",
          "gene_symbol": "MSH2",
          "hgnc_id": 7325,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.135G>A",
          "hgvs_p": "p.Ala45Ala"
        }
      ],
      "clinvar_disease": "Hereditary cancer-predisposing syndrome,Hereditary nonpolyposis colorectal neoplasms,Lynch syndrome 1,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:3 B:1",
      "phenotype_combined": "Hereditary nonpolyposis colorectal neoplasms|Hereditary cancer-predisposing syndrome|not specified|Lynch syndrome 1",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}