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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: 2-165139597-T-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165139597&ref=T&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 165139597,
      "ref": "T",
      "alt": "A",
      "effect": "synonymous_variant",
      "transcript": "ENST00000283254.12",
      "consequences": [
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.2031A>T",
          "hgvs_p": "p.Thr677Thr",
          "transcript": "NM_006922.4",
          "protein_id": "NP_008853.3",
          "transcript_support_level": null,
          "aa_start": 677,
          "aa_end": null,
          "aa_length": 2000,
          "cds_start": 2031,
          "cds_end": null,
          "cds_length": 6003,
          "cdna_start": 2506,
          "cdna_end": null,
          "cdna_length": 9102,
          "mane_select": "ENST00000283254.12",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.2031A>T",
          "hgvs_p": "p.Thr677Thr",
          "transcript": "ENST00000283254.12",
          "protein_id": "ENSP00000283254.7",
          "transcript_support_level": 1,
          "aa_start": 677,
          "aa_end": null,
          "aa_length": 2000,
          "cds_start": 2031,
          "cds_end": null,
          "cds_length": 6003,
          "cdna_start": 2506,
          "cdna_end": null,
          "cdna_length": 9102,
          "mane_select": "NM_006922.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.1884A>T",
          "hgvs_p": "p.Thr628Thr",
          "transcript": "ENST00000409101.7",
          "protein_id": "ENSP00000386726.3",
          "transcript_support_level": 1,
          "aa_start": 628,
          "aa_end": null,
          "aa_length": 1951,
          "cds_start": 1884,
          "cds_end": null,
          "cds_length": 5856,
          "cdna_start": 2195,
          "cdna_end": null,
          "cdna_length": 6599,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.1980A>T",
          "hgvs_p": "p.Thr660Thr",
          "transcript": "ENST00000706067.1",
          "protein_id": "ENSP00000516211.1",
          "transcript_support_level": null,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 1983,
          "cds_start": 1980,
          "cds_end": null,
          "cds_length": 5952,
          "cdna_start": 2289,
          "cdna_end": null,
          "cdna_length": 8869,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.1980A>T",
          "hgvs_p": "p.Thr660Thr",
          "transcript": "ENST00000639244.1",
          "protein_id": "ENSP00000492251.1",
          "transcript_support_level": 5,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 1979,
          "cds_start": 1980,
          "cds_end": null,
          "cds_length": 5940,
          "cdna_start": 2286,
          "cdna_end": null,
          "cdna_length": 8854,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.1884A>T",
          "hgvs_p": "p.Thr628Thr",
          "transcript": "NM_001081676.2",
          "protein_id": "NP_001075145.1",
          "transcript_support_level": null,
          "aa_start": 628,
          "aa_end": null,
          "aa_length": 1951,
          "cds_start": 1884,
          "cds_end": null,
          "cds_length": 5856,
          "cdna_start": 2359,
          "cdna_end": null,
          "cdna_length": 8955,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.1884A>T",
          "hgvs_p": "p.Thr628Thr",
          "transcript": "NM_001081677.2",
          "protein_id": "NP_001075146.1",
          "transcript_support_level": null,
          "aa_start": 628,
          "aa_end": null,
          "aa_length": 1951,
          "cds_start": 1884,
          "cds_end": null,
          "cds_length": 5856,
          "cdna_start": 2359,
          "cdna_end": null,
          "cdna_length": 8955,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.1884A>T",
          "hgvs_p": "p.Thr628Thr",
          "transcript": "ENST00000440431.6",
          "protein_id": "ENSP00000403348.1",
          "transcript_support_level": 5,
          "aa_start": 628,
          "aa_end": null,
          "aa_length": 1363,
          "cds_start": 1884,
          "cds_end": null,
          "cds_length": 4092,
          "cdna_start": 1938,
          "cdna_end": null,
          "cdna_length": 4146,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.1893A>T",
          "hgvs_p": "p.Thr631Thr",
          "transcript": "ENST00000668657.1",
          "protein_id": "ENSP00000499420.1",
          "transcript_support_level": null,
          "aa_start": 631,
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          "aa_length": 1086,
          "cds_start": 1893,
          "cds_end": null,
          "cds_length": 3261,
          "cdna_start": 2209,
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          "mane_select": null,
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          "biotype": null,
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        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.2031A>T",
          "hgvs_p": "p.Thr677Thr",
          "transcript": "XM_011511610.4",
          "protein_id": "XP_011509912.1",
          "transcript_support_level": null,
          "aa_start": 677,
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          "aa_length": 2000,
          "cds_start": 2031,
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          "mane_select": null,
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        },
        {
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          "strand": false,
          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "c.2031A>T",
          "hgvs_p": "p.Thr677Thr",
          "transcript": "XM_017004660.3",
          "protein_id": "XP_016860149.1",
          "transcript_support_level": null,
          "aa_start": 677,
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          "cds_start": 2031,
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        {
          "aa_ref": "T",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          "exon_rank": 14,
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          "intron_rank": null,
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          "gene_symbol": "SCN3A",
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        {
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        {
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          "strand": false,
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          "intron_rank": null,
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          "gene_symbol": "SCN3A",
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          "hgvs_c": "c.1893A>T",
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        {
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        {
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          "gene_symbol": "SCN3A",
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        {
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        {
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          "strand": false,
          "consequences": [
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          ],
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          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
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          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "n.1897A>T",
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          "transcript": "ENST00000638473.1",
          "protein_id": "ENSP00000491552.1",
          "transcript_support_level": 5,
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        },
        {
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          "canonical": false,
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          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 13,
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          "intron_rank": null,
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          "gene_symbol": "SCN3A",
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          "transcript": "ENST00000640652.1",
          "protein_id": "ENSP00000492807.1",
          "transcript_support_level": 5,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 8825,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
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          "gene_symbol": "SCN3A",
          "gene_hgnc_id": 10590,
          "hgvs_c": "n.129A>T",
          "hgvs_p": null,
          "transcript": "ENST00000658209.1",
          "protein_id": "ENSP00000499598.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 5540,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000236283",
          "gene_hgnc_id": null,
          "hgvs_c": "n.320+9393T>A",
          "hgvs_p": null,
          "transcript": "ENST00000625505.2",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 758,
          "mane_select": null,
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        },
        {
          "aa_ref": null,
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000236283",
          "gene_hgnc_id": null,
          "hgvs_c": "n.533-2T>A",
          "hgvs_p": null,
          "transcript": "ENST00000629817.2",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 980,
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          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "SCN3A",
      "gene_hgnc_id": 10590,
      "dbsnp": "rs1946892",
      "frequency_reference_population": 0.45429283,
      "hom_count_reference_population": 173086,
      "allele_count_reference_population": 732867,
      "gnomad_exomes_af": 0.447531,
      "gnomad_genomes_af": 0.519342,
      "gnomad_exomes_ac": 653980,
      "gnomad_genomes_ac": 78887,
      "gnomad_exomes_homalt": 151513,
      "gnomad_genomes_homalt": 21573,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.4699999988079071,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.47,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.072,
      "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": -21,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
      "acmg_by_gene": [
        {
          "score": -21,
          "benign_score": 21,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000283254.12",
          "gene_symbol": "SCN3A",
          "hgnc_id": 10590,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.2031A>T",
          "hgvs_p": "p.Thr677Thr"
        },
        {
          "score": -14,
          "benign_score": 16,
          "pathogenic_score": 2,
          "criteria": [
            "PVS1_Moderate",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000629817.2",
          "gene_symbol": "ENSG00000236283",
          "hgnc_id": null,
          "effects": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.533-2T>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " 62, familial focal, with variable foci 4,Developmental and epileptic encephalopathy,Epilepsy,not provided,not specified",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "B:7",
      "phenotype_combined": "not provided|Epilepsy, familial focal, with variable foci 4|Developmental and epileptic encephalopathy, 62|not specified",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}