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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: 3-93973667-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=93973667&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 93973667,
      "ref": "T",
      "alt": "C",
      "effect": "splice_region_variant,intron_variant",
      "transcript": "NM_001314077.2",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "NM_000313.4",
          "protein_id": "NP_000304.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 676,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2031,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000394236.9",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_000313.4"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000394236.9",
          "protein_id": "ENSP00000377783.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 676,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2031,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_000313.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000394236.9"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000407433.6",
          "protein_id": "ENSP00000385794.2",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 661,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1986,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000407433.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "NM_001314077.2",
          "protein_id": "NP_001301006.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 708,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2127,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001314077.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000650591.1",
          "protein_id": "ENSP00000497376.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 708,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2127,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000650591.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000869621.1",
          "protein_id": "ENSP00000539680.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 693,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2082,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000869621.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000948247.1",
          "protein_id": "ENSP00000618306.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 681,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2046,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000948247.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000348974.5",
          "protein_id": "ENSP00000330021.7",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 676,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2031,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000348974.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000948248.1",
          "protein_id": "ENSP00000618307.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 674,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2025,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000948248.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000869623.1",
          "protein_id": "ENSP00000539682.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 673,
          "cds_start": null,
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          "cds_length": 2022,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 15,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.34+5977A>G",
          "hgvs_p": null,
          "transcript": "ENST00000648853.1",
          "protein_id": "ENSP00000497262.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 662,
          "cds_start": null,
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          "cds_length": 1989,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
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        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 15,
          "intron_rank": 1,
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          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000869617.1",
          "protein_id": "ENSP00000539676.1",
          "transcript_support_level": null,
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          "aa_length": 661,
          "cds_start": null,
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          "cdna_start": null,
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        },
        {
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          "strand": false,
          "consequences": [
            "splice_region_variant",
            "intron_variant"
          ],
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          "exon_count": 14,
          "intron_rank": 1,
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          "gene_symbol": "PROS1",
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          "cds_start": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": null,
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          "canonical": false,
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          "consequences": [
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            "intron_variant"
          ],
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          "exon_count": 14,
          "intron_rank": 1,
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          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000869619.1",
          "protein_id": "ENSP00000539678.1",
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          "biotype": "protein_coding",
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        {
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          "consequences": [
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            "intron_variant"
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          "exon_count": 14,
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          "gene_symbol": "PROS1",
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          "transcript": "ENST00000869625.1",
          "protein_id": "ENSP00000539684.1",
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        {
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          "strand": false,
          "consequences": [
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            "intron_variant"
          ],
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          "exon_count": 14,
          "intron_rank": 1,
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          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
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          "transcript": "ENST00000869615.1",
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          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
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        {
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          "gene_symbol": "PROS1",
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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            "intron_variant"
          ],
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          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "PROS1",
          "gene_hgnc_id": 9456,
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null,
          "transcript": "ENST00000869618.1",
          "protein_id": "ENSP00000539677.1",
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          "biotype": "nonsense_mediated_decay",
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        {
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          "protein_coding": true,
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            "upstream_gene_variant"
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          "exon_count": 6,
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          "gene_symbol": "PROS1",
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          "hgvs_c": "c.-422A>G",
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          "transcript": "ENST00000472684.2",
          "protein_id": "ENSP00000419616.2",
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          "cds_length": 171,
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          "cdna_length": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000472684.2"
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      ],
      "gene_symbol": "PROS1",
      "gene_hgnc_id": 9456,
      "dbsnp": "rs201928951",
      "frequency_reference_population": 0.00043824143,
      "hom_count_reference_population": 4,
      "allele_count_reference_population": 707,
      "gnomad_exomes_af": 0.000427775,
      "gnomad_genomes_af": 0.000538701,
      "gnomad_exomes_ac": 625,
      "gnomad_genomes_ac": 82,
      "gnomad_exomes_homalt": 4,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.28999999165534973,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0.23800000548362732,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "dbscSNV1_RF",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.29,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 3.379,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.18,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": 0.0411472432493952,
      "dbscsnv_ada_prediction": "Benign",
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -7,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Moderate,BP6,BS2",
      "acmg_by_gene": [
        {
          "score": -7,
          "benign_score": 7,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BP6",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "NM_001314077.2",
          "gene_symbol": "PROS1",
          "hgnc_id": 9456,
          "effects": [
            "splice_region_variant",
            "intron_variant"
          ],
          "inheritance_mode": "AD,AR,SD",
          "hgvs_c": "c.76+7A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " autosomal dominant, autosomal recessive,PROS1-related disorder,Protein S deficiency disease,Thrombophilia due to protein S deficiency,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:4 LB:1 B:2",
      "phenotype_combined": "Thrombophilia due to protein S deficiency, autosomal recessive|Thrombophilia due to protein S deficiency, autosomal dominant|Protein S deficiency disease|not provided|PROS1-related disorder",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}