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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: 20-3213154-TTTCTC-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=3213154&ref=TTTCTC&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "20",
      "pos": 3213154,
      "ref": "TTTCTC",
      "alt": "T",
      "effect": "intron_variant",
      "transcript": "ENST00000380113.8",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.67-12_67-8delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_033453.4",
          "protein_id": "NP_258412.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 194,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 585,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1037,
          "mane_select": "ENST00000380113.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.67-14_67-10delTTCTC",
          "hgvs_p": null,
          "transcript": "ENST00000380113.8",
          "protein_id": "ENSP00000369456.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 194,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 585,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1037,
          "mane_select": "NM_033453.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.16-14_16-10delTTCTC",
          "hgvs_p": null,
          "transcript": "ENST00000455664.6",
          "protein_id": "ENSP00000413282.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 177,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 534,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 729,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.67-830_67-826delTTCTC",
          "hgvs_p": null,
          "transcript": "ENST00000399838.3",
          "protein_id": "ENSP00000382732.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 153,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 462,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 897,
          "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": 5,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "n.118-103_118-99delTTCTC",
          "hgvs_p": null,
          "transcript": "ENST00000609835.5",
          "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": 924,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.67-12_67-8delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_001424408.1",
          "protein_id": "NP_001411337.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 238,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 717,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1084,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.193-12_193-8delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_001424409.1",
          "protein_id": "NP_001411338.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 236,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 711,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1449,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.16-12_16-8delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_181493.4",
          "protein_id": "NP_852470.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 177,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 534,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 986,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.67-828_67-824delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_001267623.2",
          "protein_id": "NP_001254552.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 153,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 462,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 914,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.67-12_67-8delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_001324240.2",
          "protein_id": "NP_001311169.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 138,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 417,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1232,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 1,
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          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.-274-101_-274-97delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_001324236.2",
          "protein_id": "NP_001311165.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 110,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 333,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1040,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.-271-12_-271-8delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_001324237.2",
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          "transcript_support_level": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "mane_select": null,
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        {
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          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 7,
          "intron_rank": 1,
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          "gene_symbol": "ITPA",
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          "hgvs_c": "c.-274-101_-274-97delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_001324238.2",
          "protein_id": "NP_001311167.1",
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          "cds_start": -4,
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          "cdna_start": null,
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          "mane_select": null,
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        {
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.-274-101_-274-97delCTCTT",
          "hgvs_p": null,
          "transcript": "NM_001351739.2",
          "protein_id": "NP_001338668.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 110,
          "cds_start": -4,
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          "cds_length": 333,
          "cdna_start": null,
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          "cdna_length": 958,
          "mane_select": null,
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          "feature": null
        },
        {
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          "canonical": false,
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          ],
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          "intron_rank": 1,
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          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "n.106-14_106-10delTTCTC",
          "hgvs_p": null,
          "transcript": "ENST00000460550.5",
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        },
        {
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          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "n.137-14_137-10delTTCTC",
          "hgvs_p": null,
          "transcript": "ENST00000460676.5",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
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          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 488,
          "mane_select": null,
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          "feature": null
        },
        {
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          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 1,
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          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "n.167-14_167-10delTTCTC",
          "hgvs_p": null,
          "transcript": "ENST00000483354.5",
          "protein_id": null,
          "transcript_support_level": 3,
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          "cdna_length": 1028,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 7,
          "intron_rank": 1,
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          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "n.48-103_48-99delTTCTC",
          "hgvs_p": null,
          "transcript": "ENST00000490838.6",
          "protein_id": null,
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        },
        {
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          "strand": true,
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            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 7,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "n.359-12_359-8delCTCTT",
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          "transcript": "NR_052000.2",
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          "biotype": null,
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 7,
          "intron_rank": 1,
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          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "n.121-12_121-8delCTCTT",
          "hgvs_p": null,
          "transcript": "NR_052002.2",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "cds_start": -4,
          "cds_end": null,
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          "cdna_start": null,
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          "cdna_length": 972,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.193-12_193-8delCTCTT",
          "hgvs_p": null,
          "transcript": "XM_047440139.1",
          "protein_id": "XP_047296095.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 280,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 843,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 1496,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.67-828_67-824delCTCTT",
          "hgvs_p": null,
          "transcript": "XM_006723565.4",
          "protein_id": "XP_006723628.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 197,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 594,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 961,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ITPA",
          "gene_hgnc_id": 6176,
          "hgvs_c": "c.67-12_67-8delCTCTT",
          "hgvs_p": null,
          "transcript": "XM_011529234.3",
          "protein_id": "XP_011527536.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 147,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 444,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 752,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "ITPA",
      "gene_hgnc_id": 6176,
      "dbsnp": "rs771313305",
      "frequency_reference_population": 0.000032857213,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 53,
      "gnomad_exomes_af": 0.0000301205,
      "gnomad_genomes_af": 0.0000591164,
      "gnomad_exomes_ac": 44,
      "gnomad_genomes_ac": 9,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": null,
      "computational_prediction_selected": null,
      "computational_source_selected": null,
      "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": null,
      "bayesdelnoaf_prediction": null,
      "phylop100way_score": 1.209,
      "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": 0,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,BP6_Moderate",
      "acmg_by_gene": [
        {
          "score": 0,
          "benign_score": 2,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP6_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000380113.8",
          "gene_symbol": "ITPA",
          "hgnc_id": 6176,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.67-14_67-10delTTCTC",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Inosine triphosphatase deficiency",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LB:1",
      "phenotype_combined": "Inosine triphosphatase deficiency",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}