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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: 9-95447221-ACGGGCCCCGCGAGGGCCCCAG-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=95447221&ref=ACGGGCCCCGCGAGGGCCCCAG&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "9",
      "pos": 95447221,
      "ref": "ACGGGCCCCGCGAGGGCCCCAG",
      "alt": "A",
      "effect": "disruptive_inframe_deletion",
      "transcript": "ENST00000331920.11",
      "consequences": [
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.4014_4034delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1339_Arg1345del",
          "transcript": "NM_000264.5",
          "protein_id": "NP_000255.2",
          "transcript_support_level": null,
          "aa_start": 1338,
          "aa_end": null,
          "aa_length": 1447,
          "cds_start": 4014,
          "cds_end": null,
          "cds_length": 4344,
          "cdna_start": 4939,
          "cdna_end": null,
          "cdna_length": 8662,
          "mane_select": "ENST00000331920.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.4014_4034delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1339_Arg1345del",
          "transcript": "ENST00000331920.11",
          "protein_id": "ENSP00000332353.6",
          "transcript_support_level": 5,
          "aa_start": 1338,
          "aa_end": null,
          "aa_length": 1447,
          "cds_start": 4014,
          "cds_end": null,
          "cds_length": 4344,
          "cdna_start": 4939,
          "cdna_end": null,
          "cdna_length": 8662,
          "mane_select": "NM_000264.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.4011_4031delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1338_Arg1344del",
          "transcript": "NM_001083603.3",
          "protein_id": "NP_001077072.1",
          "transcript_support_level": null,
          "aa_start": 1337,
          "aa_end": null,
          "aa_length": 1446,
          "cds_start": 4011,
          "cds_end": null,
          "cds_length": 4341,
          "cdna_start": 4182,
          "cdna_end": null,
          "cdna_length": 7905,
          "mane_select": null,
          "mane_plus": "ENST00000437951.6",
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.4011_4031delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1338_Arg1344del",
          "transcript": "ENST00000437951.6",
          "protein_id": "ENSP00000389744.2",
          "transcript_support_level": 5,
          "aa_start": 1337,
          "aa_end": null,
          "aa_length": 1446,
          "cds_start": 4011,
          "cds_end": null,
          "cds_length": 4341,
          "cdna_start": 4182,
          "cdna_end": null,
          "cdna_length": 7905,
          "mane_select": null,
          "mane_plus": "NM_001083603.3",
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.3561_3581delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1188_Arg1194del",
          "transcript": "ENST00000429896.6",
          "protein_id": "ENSP00000414823.2",
          "transcript_support_level": 1,
          "aa_start": 1187,
          "aa_end": null,
          "aa_length": 1296,
          "cds_start": 3561,
          "cds_end": null,
          "cds_length": 3891,
          "cdna_start": 4022,
          "cdna_end": null,
          "cdna_length": 6563,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.3858_3878delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1287_Arg1293del",
          "transcript": "NM_001354918.2",
          "protein_id": "NP_001341847.1",
          "transcript_support_level": null,
          "aa_start": 1286,
          "aa_end": null,
          "aa_length": 1395,
          "cds_start": 3858,
          "cds_end": null,
          "cds_length": 4188,
          "cdna_start": 4783,
          "cdna_end": null,
          "cdna_length": 8506,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.3816_3836delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1273_Arg1279del",
          "transcript": "NM_001083602.3",
          "protein_id": "NP_001077071.1",
          "transcript_support_level": null,
          "aa_start": 1272,
          "aa_end": null,
          "aa_length": 1381,
          "cds_start": 3816,
          "cds_end": null,
          "cds_length": 4146,
          "cdna_start": 4336,
          "cdna_end": null,
          "cdna_length": 8059,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.3816_3836delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1273_Arg1279del",
          "transcript": "ENST00000430669.6",
          "protein_id": "ENSP00000410287.2",
          "transcript_support_level": 5,
          "aa_start": 1272,
          "aa_end": null,
          "aa_length": 1381,
          "cds_start": 3816,
          "cds_end": null,
          "cds_length": 4146,
          "cdna_start": 4422,
          "cdna_end": null,
          "cdna_length": 8232,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "RWGPRGAR",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "disruptive_inframe_deletion"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
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          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.3816_3836delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1273_Arg1279del",
          "transcript": "ENST00000711046.1",
          "protein_id": "ENSP00000518556.1",
          "transcript_support_level": null,
          "aa_start": 1272,
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          "aa_length": 1381,
          "cds_start": 3816,
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          "cds_length": 4146,
          "cdna_start": 4336,
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        },
        {
          "aa_ref": "RWGPRGAR",
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 23,
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          "exon_count": 24,
          "intron_rank": null,
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          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "c.3561_3581delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1188_Arg1194del",
          "transcript": "NM_001083604.3",
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          "aa_start": 1187,
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          "cds_start": 3561,
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          "cdna_start": 3940,
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          "mane_select": null,
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        },
        {
          "aa_ref": "RWGPRGAR",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
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          "gene_symbol": "PTCH1",
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          "hgvs_p": "p.Trp1188_Arg1194del",
          "transcript": "NM_001083605.3",
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          "gene_symbol": "PTCH1",
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          "hgvs_p": "p.Trp1188_Arg1194del",
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        {
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          ],
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          "gene_symbol": "PTCH1",
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          "hgvs_p": "p.Trp1188_Arg1194del",
          "transcript": "NM_001083607.3",
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        {
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "n.*5859_*5879delCTGGGGCCCTCGCGGGGCCCG",
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          "transcript": "ENST00000375290.6",
          "protein_id": "ENSP00000364439.2",
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        {
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          ],
          "exon_rank": 2,
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          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "n.1078_1098delCTGGGGCCCTCGCGGGGCCCG",
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          "transcript": "ENST00000546744.5",
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        },
        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
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        {
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          "intron_rank": null,
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          "gene_symbol": "PTCH1",
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          "protein_id": "ENSP00000509379.1",
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        },
        {
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          "consequences": [
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          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
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          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "n.1361_1381delCTGGGGCCCTCGCGGGGCCCG",
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          "transcript": "ENST00000693534.1",
          "protein_id": null,
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          "cdna_length": 4653,
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        },
        {
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          "consequences": [
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          ],
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          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "n.4753_4773delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": null,
          "transcript": "NR_149061.2",
          "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": 8496,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "n.*5859_*5879delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": null,
          "transcript": "ENST00000375290.6",
          "protein_id": "ENSP00000364439.2",
          "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": 10631,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "PTCH1",
          "gene_hgnc_id": 9585,
          "hgvs_c": "n.*2322_*2342delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": null,
          "transcript": "ENST00000690194.1",
          "protein_id": "ENSP00000509379.1",
          "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": 7135,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "PTCH1",
      "gene_hgnc_id": 9585,
      "dbsnp": "rs774819810",
      "frequency_reference_population": 0.0004241161,
      "hom_count_reference_population": 2,
      "allele_count_reference_population": 684,
      "gnomad_exomes_af": 0.00045256,
      "gnomad_genomes_af": 0.000151131,
      "gnomad_exomes_ac": 661,
      "gnomad_genomes_ac": 23,
      "gnomad_exomes_homalt": 2,
      "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": 5.646,
      "phylop100way_prediction": "Uncertain_significance",
      "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": -7,
      "acmg_classification": "Benign",
      "acmg_criteria": "PM4,BP6,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -7,
          "benign_score": 9,
          "pathogenic_score": 2,
          "criteria": [
            "PM4",
            "BP6",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000331920.11",
          "gene_symbol": "PTCH1",
          "hgnc_id": 9585,
          "effects": [
            "disruptive_inframe_deletion"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.4014_4034delCTGGGGCCCTCGCGGGGCCCG",
          "hgvs_p": "p.Trp1339_Arg1345del"
        }
      ],
      "clinvar_disease": " 1, susceptibility to,Basal cell carcinoma,Basal cell nevus syndrome 1,Gorlin syndrome,Hereditary cancer-predisposing syndrome,Holoprosencephaly 7,Intellectual disability,PTCH1-related disorder,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:2 LB:1 B:3",
      "phenotype_combined": "Gorlin syndrome|Hereditary cancer-predisposing syndrome|not provided|PTCH1-related disorder|Basal cell carcinoma, susceptibility to, 1;Holoprosencephaly 7;Basal cell nevus syndrome 1|Intellectual disability",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}