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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: 3-121993223-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=121993223&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 121993223,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_001199799.2",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1526C>T",
          "hgvs_p": "p.Pro509Leu",
          "transcript": "NM_001199799.2",
          "protein_id": "NP_001186728.1",
          "transcript_support_level": null,
          "aa_start": 509,
          "aa_end": null,
          "aa_length": 546,
          "cds_start": 1526,
          "cds_end": null,
          "cds_length": 1641,
          "cdna_start": 1696,
          "cdna_end": null,
          "cdna_length": 2855,
          "mane_select": "ENST00000344209.10",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1526C>T",
          "hgvs_p": "p.Pro509Leu",
          "transcript": "ENST00000344209.10",
          "protein_id": "ENSP00000345667.5",
          "transcript_support_level": 1,
          "aa_start": 509,
          "aa_end": null,
          "aa_length": 546,
          "cds_start": 1526,
          "cds_end": null,
          "cds_length": 1641,
          "cdna_start": 1696,
          "cdna_end": null,
          "cdna_length": 2855,
          "mane_select": "NM_001199799.2",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1394C>T",
          "hgvs_p": "p.Pro465Leu",
          "transcript": "ENST00000273691.7",
          "protein_id": "ENSP00000273691.3",
          "transcript_support_level": 1,
          "aa_start": 465,
          "aa_end": null,
          "aa_length": 502,
          "cds_start": 1394,
          "cds_end": null,
          "cds_length": 1509,
          "cdna_start": 1500,
          "cdna_end": null,
          "cdna_length": 2659,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1259C>T",
          "hgvs_p": "p.Pro420Leu",
          "transcript": "ENST00000393631.5",
          "protein_id": "ENSP00000377251.1",
          "transcript_support_level": 1,
          "aa_start": 420,
          "aa_end": null,
          "aa_length": 457,
          "cds_start": 1259,
          "cds_end": null,
          "cds_length": 1374,
          "cdna_start": 1304,
          "cdna_end": null,
          "cdna_length": 1456,
          "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": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "n.1476C>T",
          "hgvs_p": null,
          "transcript": "ENST00000460554.2",
          "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": 1612,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1394C>T",
          "hgvs_p": "p.Pro465Leu",
          "transcript": "NM_175924.4",
          "protein_id": "NP_787120.1",
          "transcript_support_level": null,
          "aa_start": 465,
          "aa_end": null,
          "aa_length": 502,
          "cds_start": 1394,
          "cds_end": null,
          "cds_length": 1509,
          "cdna_start": 1564,
          "cdna_end": null,
          "cdna_length": 2723,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1259C>T",
          "hgvs_p": "p.Pro420Leu",
          "transcript": "NM_001199800.2",
          "protein_id": "NP_001186729.1",
          "transcript_support_level": null,
          "aa_start": 420,
          "aa_end": null,
          "aa_length": 457,
          "cds_start": 1259,
          "cds_end": null,
          "cds_length": 1374,
          "cdna_start": 1429,
          "cdna_end": null,
          "cdna_length": 2588,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1526C>T",
          "hgvs_p": "p.Pro509Leu",
          "transcript": "XM_011512738.3",
          "protein_id": "XP_011511040.1",
          "transcript_support_level": null,
          "aa_start": 509,
          "aa_end": null,
          "aa_length": 525,
          "cds_start": 1526,
          "cds_end": null,
          "cds_length": 1578,
          "cdna_start": 1696,
          "cdna_end": null,
          "cdna_length": 2814,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1430C>T",
          "hgvs_p": "p.Pro477Leu",
          "transcript": "XM_005247389.5",
          "protein_id": "XP_005247446.1",
          "transcript_support_level": null,
          "aa_start": 477,
          "aa_end": null,
          "aa_length": 514,
          "cds_start": 1430,
          "cds_end": null,
          "cds_length": 1545,
          "cdna_start": 2010,
          "cdna_end": null,
          "cdna_length": 3169,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1394C>T",
          "hgvs_p": "p.Pro465Leu",
          "transcript": "XM_047448043.1",
          "protein_id": "XP_047303999.1",
          "transcript_support_level": null,
          "aa_start": 465,
          "aa_end": null,
          "aa_length": 481,
          "cds_start": 1394,
          "cds_end": null,
          "cds_length": 1446,
          "cdna_start": 1564,
          "cdna_end": null,
          "cdna_length": 2682,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "c.1121C>T",
          "hgvs_p": "p.Pro374Leu",
          "transcript": "XM_047448044.1",
          "protein_id": "XP_047304000.1",
          "transcript_support_level": null,
          "aa_start": 374,
          "aa_end": null,
          "aa_length": 411,
          "cds_start": 1121,
          "cds_end": null,
          "cds_length": 1236,
          "cdna_start": 2704,
          "cdna_end": null,
          "cdna_length": 3863,
          "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": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "n.*709C>T",
          "hgvs_p": null,
          "transcript": "ENST00000642615.1",
          "protein_id": "ENSP00000495499.1",
          "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": 1704,
          "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": 7,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ILDR1",
          "gene_hgnc_id": 28741,
          "hgvs_c": "n.*709C>T",
          "hgvs_p": null,
          "transcript": "ENST00000642615.1",
          "protein_id": "ENSP00000495499.1",
          "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": 1704,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "ILDR1",
      "gene_hgnc_id": 28741,
      "dbsnp": "rs374884043",
      "frequency_reference_population": 0.000043370506,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 70,
      "gnomad_exomes_af": 0.000041734,
      "gnomad_genomes_af": 0.0000590698,
      "gnomad_exomes_ac": 61,
      "gnomad_genomes_ac": 9,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.2962625026702881,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.39,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.3257,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.02,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 4.91,
      "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": 1,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,BP4",
      "acmg_by_gene": [
        {
          "score": 1,
          "benign_score": 1,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_001199799.2",
          "gene_symbol": "ILDR1",
          "hgnc_id": 28741,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1526C>T",
          "hgvs_p": "p.Pro509Leu"
        }
      ],
      "clinvar_disease": "Inborn genetic diseases,not provided,not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "US:5",
      "phenotype_combined": "not provided|not specified|Inborn genetic diseases",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}