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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: 3-2642673-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=2642673&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 2642673,
      "ref": "A",
      "alt": "G",
      "effect": "intron_variant",
      "transcript": "NM_175607.3",
      "consequences": [
        {
          "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": 25,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "NM_175607.3",
          "protein_id": "NP_783200.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1026,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3081,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5159,
          "mane_select": "ENST00000418658.6",
          "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": 25,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000418658.6",
          "protein_id": "ENSP00000396010.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1026,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3081,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5159,
          "mane_select": "NM_175607.3",
          "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": 24,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "NM_001206955.2",
          "protein_id": "NP_001193884.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1026,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3081,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5204,
          "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": 25,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "NM_001350095.2",
          "protein_id": "NP_001337024.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1026,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3081,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5453,
          "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": 24,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000397461.5",
          "protein_id": "ENSP00000380602.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1026,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3081,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5198,
          "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": 22,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000427331.5",
          "protein_id": "ENSP00000413642.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1026,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3081,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4980,
          "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": 5,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.109+13094A>G",
          "hgvs_p": null,
          "transcript": "ENST00000434053.5",
          "protein_id": "ENSP00000404085.1",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 136,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 412,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 528,
          "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": 5,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000422330.5",
          "protein_id": "ENSP00000408594.1",
          "transcript_support_level": 4,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 115,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 348,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 658,
          "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": 5,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000455083.5",
          "protein_id": "ENSP00000390560.1",
          "transcript_support_level": 4,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 53,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 164,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 566,
          "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": 21,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "n.55+71115A>G",
          "hgvs_p": null,
          "transcript": "ENST00000427741.5",
          "protein_id": "ENSP00000396719.1",
          "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,
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          "cdna_length": 3057,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
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          "exon_rank": null,
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          "exon_count": 16,
          "intron_rank": 2,
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          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "n.252+71115A>G",
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          "transcript": "ENST00000430505.6",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 2637,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
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          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
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          "exon_rank": null,
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          "exon_count": 12,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "n.491+71115A>G",
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          "transcript": "ENST00000438282.6",
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          "cds_start": -4,
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        {
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          "canonical": false,
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          "intron_rank": 3,
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          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
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          "transcript": "XM_011533425.4",
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        {
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          "gene_symbol": "CNTN4",
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          "hgvs_c": "c.55+71115A>G",
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          "transcript": "XM_011533427.3",
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        {
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          "gene_symbol": "CNTN4",
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          "gene_symbol": "CNTN4",
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          "hgvs_c": "c.55+71115A>G",
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          "transcript": "XM_011533429.3",
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          "gene_symbol": "CNTN4",
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        {
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          "canonical": false,
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          "intron_rank": 5,
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          "gene_symbol": "CNTN4",
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          "canonical": false,
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          "intron_rank": 3,
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          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
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          "transcript": "XM_047447516.1",
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          "hgvs_p": null,
          "transcript": "XM_017005787.2",
          "protein_id": "XP_016861276.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1025,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3078,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5329,
          "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": 27,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "XM_047447535.1",
          "protein_id": "XP_047303491.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1025,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3078,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 80633,
          "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": 25,
          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "CNTN4",
          "gene_hgnc_id": 2174,
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null,
          "transcript": "XM_047447536.1",
          "protein_id": "XP_047303492.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1025,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3078,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5450,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "CNTN4",
      "gene_hgnc_id": 2174,
      "dbsnp": "rs2728076",
      "frequency_reference_population": 0.5477544,
      "hom_count_reference_population": 23111,
      "allele_count_reference_population": 83251,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": 0.547754,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": 83251,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": 23111,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.8899999856948853,
      "computational_prediction_selected": "Benign",
      "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": -0.89,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.655,
      "phylop100way_prediction": "Benign",
      "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": -14,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
      "acmg_by_gene": [
        {
          "score": -14,
          "benign_score": 14,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Moderate",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "NM_175607.3",
          "gene_symbol": "CNTN4",
          "hgnc_id": 2174,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.55+71115A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not provided",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "B:1",
      "phenotype_combined": "not provided",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}