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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: 11-78106895-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=78106895&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "11",
      "pos": 78106895,
      "ref": "G",
      "alt": "A",
      "effect": "stop_gained",
      "transcript": "NM_001425224.1",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1090C>T",
          "hgvs_p": "p.Arg364*",
          "transcript": "NM_024079.5",
          "protein_id": "NP_076984.2",
          "transcript_support_level": null,
          "aa_start": 364,
          "aa_end": null,
          "aa_length": 526,
          "cds_start": 1090,
          "cds_end": null,
          "cds_length": 1581,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000299626.10",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_024079.5"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1090C>T",
          "hgvs_p": "p.Arg364*",
          "transcript": "ENST00000299626.10",
          "protein_id": "ENSP00000299626.5",
          "transcript_support_level": 1,
          "aa_start": 364,
          "aa_end": null,
          "aa_length": 526,
          "cds_start": 1090,
          "cds_end": null,
          "cds_length": 1581,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_024079.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000299626.10"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1090C>T",
          "hgvs_p": "p.Arg364*",
          "transcript": "ENST00000679559.1",
          "protein_id": "ENSP00000505433.1",
          "transcript_support_level": null,
          "aa_start": 364,
          "aa_end": null,
          "aa_length": 560,
          "cds_start": 1090,
          "cds_end": null,
          "cds_length": 1683,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000679559.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1183C>T",
          "hgvs_p": "p.Arg395*",
          "transcript": "NM_001425224.1",
          "protein_id": "NP_001412153.1",
          "transcript_support_level": null,
          "aa_start": 395,
          "aa_end": null,
          "aa_length": 557,
          "cds_start": 1183,
          "cds_end": null,
          "cds_length": 1674,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001425224.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1138C>T",
          "hgvs_p": "p.Arg380*",
          "transcript": "NM_001425225.1",
          "protein_id": "NP_001412154.1",
          "transcript_support_level": null,
          "aa_start": 380,
          "aa_end": null,
          "aa_length": 542,
          "cds_start": 1138,
          "cds_end": null,
          "cds_length": 1629,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001425225.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1138C>T",
          "hgvs_p": "p.Arg380*",
          "transcript": "ENST00000532440.6",
          "protein_id": "ENSP00000433429.2",
          "transcript_support_level": 3,
          "aa_start": 380,
          "aa_end": null,
          "aa_length": 542,
          "cds_start": 1138,
          "cds_end": null,
          "cds_length": 1629,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000532440.6"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1090C>T",
          "hgvs_p": "p.Arg364*",
          "transcript": "NM_001425222.1",
          "protein_id": "NP_001412151.1",
          "transcript_support_level": null,
          "aa_start": 364,
          "aa_end": null,
          "aa_length": 534,
          "cds_start": 1090,
          "cds_end": null,
          "cds_length": 1605,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001425222.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1111C>T",
          "hgvs_p": "p.Arg371*",
          "transcript": "ENST00000853774.1",
          "protein_id": "ENSP00000523833.1",
          "transcript_support_level": null,
          "aa_start": 371,
          "aa_end": null,
          "aa_length": 533,
          "cds_start": 1111,
          "cds_end": null,
          "cds_length": 1602,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853774.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1093C>T",
          "hgvs_p": "p.Arg365*",
          "transcript": "NM_001425219.1",
          "protein_id": "NP_001412148.1",
          "transcript_support_level": null,
          "aa_start": 365,
          "aa_end": null,
          "aa_length": 527,
          "cds_start": 1093,
          "cds_end": null,
          "cds_length": 1584,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001425219.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1093C>T",
          "hgvs_p": "p.Arg365*",
          "transcript": "ENST00000680256.1",
          "protein_id": "ENSP00000505074.1",
          "transcript_support_level": null,
          "aa_start": 365,
          "aa_end": null,
          "aa_length": 527,
          "cds_start": 1093,
          "cds_end": null,
          "cds_length": 1584,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000680256.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1084C>T",
          "hgvs_p": "p.Arg362*",
          "transcript": "NM_001425223.1",
          "protein_id": "NP_001412152.1",
          "transcript_support_level": null,
          "aa_start": 362,
          "aa_end": null,
          "aa_length": 524,
          "cds_start": 1084,
          "cds_end": null,
          "cds_length": 1575,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001425223.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1075C>T",
          "hgvs_p": "p.Arg359*",
          "transcript": "NM_001425220.1",
          "protein_id": "NP_001412149.1",
          "transcript_support_level": null,
          "aa_start": 359,
          "aa_end": null,
          "aa_length": 521,
          "cds_start": 1075,
          "cds_end": null,
          "cds_length": 1566,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001425220.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1075C>T",
          "hgvs_p": "p.Arg359*",
          "transcript": "ENST00000853769.1",
          "protein_id": "ENSP00000523828.1",
          "transcript_support_level": null,
          "aa_start": 359,
          "aa_end": null,
          "aa_length": 521,
          "cds_start": 1075,
          "cds_end": null,
          "cds_length": 1566,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853769.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1015C>T",
          "hgvs_p": "p.Arg339*",
          "transcript": "NM_001425221.1",
          "protein_id": "NP_001412150.1",
          "transcript_support_level": null,
          "aa_start": 339,
          "aa_end": null,
          "aa_length": 501,
          "cds_start": 1015,
          "cds_end": null,
          "cds_length": 1506,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001425221.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1015C>T",
          "hgvs_p": "p.Arg339*",
          "transcript": "ENST00000853773.1",
          "protein_id": "ENSP00000523832.1",
          "transcript_support_level": null,
          "aa_start": 339,
          "aa_end": null,
          "aa_length": 501,
          "cds_start": 1015,
          "cds_end": null,
          "cds_length": 1506,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853773.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.994C>T",
          "hgvs_p": "p.Arg332*",
          "transcript": "ENST00000526849.6",
          "protein_id": "ENSP00000434388.2",
          "transcript_support_level": 2,
          "aa_start": 332,
          "aa_end": null,
          "aa_length": 494,
          "cds_start": 994,
          "cds_end": null,
          "cds_length": 1485,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000526849.6"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1090C>T",
          "hgvs_p": "p.Arg364*",
          "transcript": "ENST00000680398.1",
          "protein_id": "ENSP00000506189.1",
          "transcript_support_level": null,
          "aa_start": 364,
          "aa_end": null,
          "aa_length": 494,
          "cds_start": 1090,
          "cds_end": null,
          "cds_length": 1485,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000680398.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.946C>T",
          "hgvs_p": "p.Arg316*",
          "transcript": "ENST00000853770.1",
          "protein_id": "ENSP00000523829.1",
          "transcript_support_level": null,
          "aa_start": 316,
          "aa_end": null,
          "aa_length": 478,
          "cds_start": 946,
          "cds_end": null,
          "cds_length": 1437,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853770.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.1090C>T",
          "hgvs_p": "p.Arg364*",
          "transcript": "ENST00000965607.1",
          "protein_id": "ENSP00000635666.1",
          "transcript_support_level": null,
          "aa_start": 364,
          "aa_end": null,
          "aa_length": 477,
          "cds_start": 1090,
          "cds_end": null,
          "cds_length": 1434,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000965607.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ALG8",
          "gene_hgnc_id": 23161,
          "hgvs_c": "c.940C>T",
          "hgvs_p": "p.Arg314*",
          "transcript": "ENST00000853772.1",
          "protein_id": "ENSP00000523831.1",
          "transcript_support_level": null,
          "aa_start": 314,
          "aa_end": null,
          "aa_length": 476,
          "cds_start": 940,
          "cds_end": null,
          "cds_length": 1431,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000853772.1"
        },
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          "biotype": "pseudogene",
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      ],
      "gene_symbol": "ALG8",
      "gene_hgnc_id": 23161,
      "dbsnp": "rs376161880",
      "frequency_reference_population": 0.000082400904,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 133,
      "gnomad_exomes_af": 0.0000814046,
      "gnomad_genomes_af": 0.0000919685,
      "gnomad_exomes_ac": 119,
      "gnomad_genomes_ac": 14,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.6299999952316284,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.63,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 6.756,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 16,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PVS1,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 16,
          "benign_score": 0,
          "pathogenic_score": 16,
          "criteria": [
            "PVS1",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "NM_001425224.1",
          "gene_symbol": "ALG8",
          "hgnc_id": 23161,
          "effects": [
            "stop_gained"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.1183C>T",
          "hgvs_p": "p.Arg395*"
        }
      ],
      "clinvar_disease": "ALG8 congenital disorder of glycosylation,ALG8-related disorder,Autosomal dominant polycystic liver disease,Familial cystic renal disease,Inborn genetic diseases,Polycystic liver disease 3 with or without kidney cysts,See cases,not provided",
      "clinvar_classification": "Pathogenic/Likely pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:13 LP:1",
      "phenotype_combined": "not provided|Polycystic liver disease 3 with or without kidney cysts|Polycystic liver disease 3 with or without kidney cysts;ALG8 congenital disorder of glycosylation|ALG8 congenital disorder of glycosylation|See cases|Inborn genetic diseases|Autosomal dominant polycystic liver disease|ALG8-related disorder|Familial cystic renal disease",
      "pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}