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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: 5-137882069-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=137882069&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "5",
      "pos": 137882069,
      "ref": "G",
      "alt": "A",
      "effect": "synonymous_variant",
      "transcript": "ENST00000239926.9",
      "consequences": [
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "c.780G>A",
          "hgvs_p": "p.Ser260Ser",
          "transcript": "NM_006790.3",
          "protein_id": "NP_006781.1",
          "transcript_support_level": null,
          "aa_start": 260,
          "aa_end": null,
          "aa_length": 498,
          "cds_start": 780,
          "cds_end": null,
          "cds_length": 1497,
          "cdna_start": 1085,
          "cdna_end": null,
          "cdna_length": 2268,
          "mane_select": "ENST00000239926.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "c.780G>A",
          "hgvs_p": "p.Ser260Ser",
          "transcript": "ENST00000239926.9",
          "protein_id": "ENSP00000239926.4",
          "transcript_support_level": 1,
          "aa_start": 260,
          "aa_end": null,
          "aa_length": 498,
          "cds_start": 780,
          "cds_end": null,
          "cds_length": 1497,
          "cdna_start": 1085,
          "cdna_end": null,
          "cdna_length": 2268,
          "mane_select": "NM_006790.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "c.435G>A",
          "hgvs_p": "p.Ser145Ser",
          "transcript": "NM_001300911.2",
          "protein_id": "NP_001287840.1",
          "transcript_support_level": null,
          "aa_start": 145,
          "aa_end": null,
          "aa_length": 383,
          "cds_start": 435,
          "cds_end": null,
          "cds_length": 1152,
          "cdna_start": 734,
          "cdna_end": null,
          "cdna_length": 1917,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "c.435G>A",
          "hgvs_p": "p.Ser145Ser",
          "transcript": "ENST00000515645.1",
          "protein_id": "ENSP00000426281.1",
          "transcript_support_level": 2,
          "aa_start": 145,
          "aa_end": null,
          "aa_length": 383,
          "cds_start": 435,
          "cds_end": null,
          "cds_length": 1152,
          "cdna_start": 718,
          "cdna_end": null,
          "cdna_length": 1578,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "c.228G>A",
          "hgvs_p": "p.Ser76Ser",
          "transcript": "NM_001135940.2",
          "protein_id": "NP_001129412.1",
          "transcript_support_level": null,
          "aa_start": 76,
          "aa_end": null,
          "aa_length": 314,
          "cds_start": 228,
          "cds_end": null,
          "cds_length": 945,
          "cdna_start": 603,
          "cdna_end": null,
          "cdna_length": 1786,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "c.228G>A",
          "hgvs_p": "p.Ser76Ser",
          "transcript": "ENST00000421631.6",
          "protein_id": "ENSP00000391185.2",
          "transcript_support_level": 2,
          "aa_start": 76,
          "aa_end": null,
          "aa_length": 314,
          "cds_start": 228,
          "cds_end": null,
          "cds_length": 945,
          "cdna_start": 605,
          "cdna_end": null,
          "cdna_length": 1474,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "c.195G>A",
          "hgvs_p": "p.Ser65Ser",
          "transcript": "XM_017010061.2",
          "protein_id": "XP_016865550.1",
          "transcript_support_level": null,
          "aa_start": 65,
          "aa_end": null,
          "aa_length": 303,
          "cds_start": 195,
          "cds_end": null,
          "cds_length": 912,
          "cdna_start": 334,
          "cdna_end": null,
          "cdna_length": 1517,
          "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": 2,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "n.345G>A",
          "hgvs_p": null,
          "transcript": "ENST00000503748.1",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": 582,
          "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": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.1930C>T",
          "hgvs_p": null,
          "transcript": "ENST00000508281.3",
          "protein_id": null,
          "transcript_support_level": 2,
          "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": 4275,
          "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": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.1855C>T",
          "hgvs_p": null,
          "transcript": "XR_007058950.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 8495,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "n.506+1204G>A",
          "hgvs_p": null,
          "transcript": "ENST00000509812.5",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 563,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "MYOT",
          "gene_hgnc_id": 12399,
          "hgvs_c": "n.251+1204G>A",
          "hgvs_p": null,
          "transcript": "ENST00000511254.1",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 579,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.370+6091C>T",
          "hgvs_p": null,
          "transcript": "ENST00000514616.7",
          "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,
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          "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": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.317+6091C>T",
          "hgvs_p": null,
          "transcript": "ENST00000728404.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 1128,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.301+6091C>T",
          "hgvs_p": null,
          "transcript": "ENST00000728405.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cdna_length": 1953,
          "mane_select": null,
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        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.308+6091C>T",
          "hgvs_p": null,
          "transcript": "ENST00000728406.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 1228,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.361+6091C>T",
          "hgvs_p": null,
          "transcript": "ENST00000728407.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 942,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.302+6091C>T",
          "hgvs_p": null,
          "transcript": "ENST00000728408.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.188+7078C>T",
          "hgvs_p": null,
          "transcript": "ENST00000728409.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 755,
          "mane_select": null,
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          "biotype": null,
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.186+7078C>T",
          "hgvs_p": null,
          "transcript": "ENST00000728410.1",
          "protein_id": null,
          "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,
          "cdna_end": null,
          "cdna_length": 625,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "PKD2L2-DT",
          "gene_hgnc_id": 55557,
          "hgvs_c": "n.356+6091C>T",
          "hgvs_p": null,
          "transcript": "ENST00000728411.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 781,
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      ],
      "gene_symbol": "MYOT",
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      "dbsnp": "rs116773838",
      "frequency_reference_population": 0.0027965496,
      "hom_count_reference_population": 112,
      "allele_count_reference_population": 4514,
      "gnomad_exomes_af": 0.00154189,
      "gnomad_genomes_af": 0.0148401,
      "gnomad_exomes_ac": 2254,
      "gnomad_genomes_ac": 2260,
      "gnomad_exomes_homalt": 61,
      "gnomad_genomes_homalt": 51,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.550000011920929,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0.03999999910593033,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.55,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -1.628,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.04,
      "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": "ENST00000239926.9",
          "gene_symbol": "MYOT",
          "hgnc_id": 12399,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.780G>A",
          "hgvs_p": "p.Ser260Ser"
        },
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000508281.3",
          "gene_symbol": "PKD2L2-DT",
          "hgnc_id": 55557,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.1930C>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " Dominant,Limb-Girdle Muscular Dystrophy,Myofibrillar myopathy 3,not provided,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2 B:8",
      "phenotype_combined": "not specified|Limb-Girdle Muscular Dystrophy, Dominant|not provided|Myofibrillar myopathy 3",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}