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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: 6-57946158-C-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=57946158&ref=C&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "6",
      "pos": 57946158,
      "ref": "C",
      "alt": "A",
      "effect": "non_coding_transcript_exon_variant",
      "transcript": "ENST00000399751.7",
      "consequences": [
        {
          "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": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1589G>T",
          "hgvs_p": null,
          "transcript": "ENST00000399751.7",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1913,
          "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": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1509G>T",
          "hgvs_p": null,
          "transcript": "ENST00000450081.6",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1833,
          "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": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1649G>T",
          "hgvs_p": null,
          "transcript": "ENST00000418368.2",
          "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": 1978,
          "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": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1518G>T",
          "hgvs_p": null,
          "transcript": "ENST00000418765.7",
          "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": 1844,
          "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": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.2547G>T",
          "hgvs_p": null,
          "transcript": "ENST00000422882.1",
          "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": 2622,
          "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": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1397G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841711.1",
          "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": 1676,
          "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": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1408G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841712.1",
          "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": 1654,
          "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": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.513G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841713.1",
          "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": 589,
          "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": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1363G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841714.1",
          "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": 1439,
          "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": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1455G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841715.1",
          "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": 1531,
          "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": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.768G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841716.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 844,
          "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": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1388G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841717.1",
          "protein_id": null,
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          "cdna_start": null,
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          "mane_select": null,
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        {
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          "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": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.380G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841718.1",
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          "cdna_length": 460,
          "mane_select": null,
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        {
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          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
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          "intron_rank": null,
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          "gene_symbol": "LINC00680",
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          "hgvs_c": "n.1398G>T",
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          "protein_id": null,
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          "cdna_length": 1478,
          "mane_select": null,
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        },
        {
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          "protein_coding": false,
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          "consequences": [
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          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
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          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.307G>T",
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          ],
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          "exon_count": 6,
          "intron_rank": null,
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          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.849G>T",
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          "transcript": "ENST00000841721.1",
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          "cdna_length": 925,
          "mane_select": null,
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        },
        {
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1324G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841722.1",
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        {
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
          "gene_hgnc_id": null,
          "hgvs_c": "n.1329G>T",
          "hgvs_p": null,
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          "exon_count": 4,
          "intron_rank": null,
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          "gene_symbol": "LINC00680",
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          ],
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          "intron_rank": null,
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          "gene_symbol": "LINC00680",
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          "hgvs_c": "n.1328G>T",
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          "transcript": "ENST00000842094.1",
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        },
        {
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          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
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          "hgvs_c": "n.2196G>T",
          "hgvs_p": null,
          "transcript": "ENST00000842095.1",
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        {
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          "cds_length": null,
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        },
        {
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          "protein_coding": false,
          "strand": false,
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          ],
          "exon_rank": null,
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          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680",
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          "hgvs_c": "n.265-1161G>T",
          "hgvs_p": null,
          "transcript": "ENST00000841709.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 530,
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        },
        {
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          "canonical": false,
          "protein_coding": false,
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          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 7,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680-GUSBP4",
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          "hgvs_c": "n.283+12870G>T",
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          "transcript": "NR_003660.2",
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          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 770,
          "mane_select": null,
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          "feature": null
        },
        {
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          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 9,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680-GUSBP4",
          "gene_hgnc_id": 56755,
          "hgvs_c": "n.542+2760G>T",
          "hgvs_p": null,
          "transcript": "NR_132997.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cdna_start": null,
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          "cdna_length": 1029,
          "mane_select": null,
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          "feature": null
        },
        {
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          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 6,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "LINC00680-GUSBP4",
          "gene_hgnc_id": 56755,
          "hgvs_c": "n.210+12870G>T",
          "hgvs_p": null,
          "transcript": "NR_132998.1",
          "protein_id": null,
          "transcript_support_level": null,
          "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": 697,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "LINC00680",
      "gene_hgnc_id": null,
      "dbsnp": "rs15680",
      "frequency_reference_population": 0.0000065874415,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": 0.00000658744,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.8700000047683716,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": null,
      "splice_prediction_selected": null,
      "splice_source_selected": null,
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.87,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.076,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": null,
      "spliceai_max_prediction": null,
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -2,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PM2,BP4_Strong",
      "acmg_by_gene": [
        {
          "score": -2,
          "benign_score": 4,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000399751.7",
          "gene_symbol": "LINC00680",
          "hgnc_id": null,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.1589G>T",
          "hgvs_p": null
        },
        {
          "score": -2,
          "benign_score": 4,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "NR_003660.2",
          "gene_symbol": "LINC00680-GUSBP4",
          "hgnc_id": 56755,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.283+12870G>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}