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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: 1-11793961-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=11793961&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 11793961,
      "ref": "C",
      "alt": "T",
      "effect": "synonymous_variant",
      "transcript": "ENST00000376590.9",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1476G>A",
          "hgvs_p": "p.Pro492Pro",
          "transcript": "NM_005957.5",
          "protein_id": "NP_005948.3",
          "transcript_support_level": null,
          "aa_start": 492,
          "aa_end": null,
          "aa_length": 656,
          "cds_start": 1476,
          "cds_end": null,
          "cds_length": 1971,
          "cdna_start": 1566,
          "cdna_end": null,
          "cdna_length": 7018,
          "mane_select": "ENST00000376590.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1476G>A",
          "hgvs_p": "p.Pro492Pro",
          "transcript": "ENST00000376590.9",
          "protein_id": "ENSP00000365775.3",
          "transcript_support_level": 1,
          "aa_start": 492,
          "aa_end": null,
          "aa_length": 656,
          "cds_start": 1476,
          "cds_end": null,
          "cds_length": 1971,
          "cdna_start": 1566,
          "cdna_end": null,
          "cdna_length": 7018,
          "mane_select": "NM_005957.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1596G>A",
          "hgvs_p": "p.Pro532Pro",
          "transcript": "ENST00000423400.7",
          "protein_id": "ENSP00000398908.3",
          "transcript_support_level": 1,
          "aa_start": 532,
          "aa_end": null,
          "aa_length": 696,
          "cds_start": 1596,
          "cds_end": null,
          "cds_length": 2091,
          "cdna_start": 1608,
          "cdna_end": null,
          "cdna_length": 2715,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1476G>A",
          "hgvs_p": "p.Pro492Pro",
          "transcript": "ENST00000376592.6",
          "protein_id": "ENSP00000365777.1",
          "transcript_support_level": 1,
          "aa_start": 492,
          "aa_end": null,
          "aa_length": 656,
          "cds_start": 1476,
          "cds_end": null,
          "cds_length": 1971,
          "cdna_start": 2926,
          "cdna_end": null,
          "cdna_length": 8378,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1599G>A",
          "hgvs_p": "p.Pro533Pro",
          "transcript": "NM_001330358.2",
          "protein_id": "NP_001317287.1",
          "transcript_support_level": null,
          "aa_start": 533,
          "aa_end": null,
          "aa_length": 697,
          "cds_start": 1599,
          "cds_end": null,
          "cds_length": 2094,
          "cdna_start": 1622,
          "cdna_end": null,
          "cdna_length": 7074,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1599G>A",
          "hgvs_p": "p.Pro533Pro",
          "transcript": "ENST00000376583.7",
          "protein_id": "ENSP00000365767.3",
          "transcript_support_level": 5,
          "aa_start": 533,
          "aa_end": null,
          "aa_length": 697,
          "cds_start": 1599,
          "cds_end": null,
          "cds_length": 2094,
          "cdna_start": 1599,
          "cdna_end": null,
          "cdna_length": 7044,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1599G>A",
          "hgvs_p": "p.Pro533Pro",
          "transcript": "ENST00000376585.6",
          "protein_id": "ENSP00000365770.1",
          "transcript_support_level": 5,
          "aa_start": 533,
          "aa_end": null,
          "aa_length": 697,
          "cds_start": 1599,
          "cds_end": null,
          "cds_length": 2094,
          "cdna_start": 2651,
          "cdna_end": null,
          "cdna_length": 8094,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1596G>A",
          "hgvs_p": "p.Pro532Pro",
          "transcript": "NM_001410750.1",
          "protein_id": "NP_001397679.1",
          "transcript_support_level": null,
          "aa_start": 532,
          "aa_end": null,
          "aa_length": 696,
          "cds_start": 1596,
          "cds_end": null,
          "cds_length": 2091,
          "cdna_start": 1619,
          "cdna_end": null,
          "cdna_length": 7071,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1476G>A",
          "hgvs_p": "p.Pro492Pro",
          "transcript": "ENST00000641407.1",
          "protein_id": "ENSP00000493098.1",
          "transcript_support_level": null,
          "aa_start": 492,
          "aa_end": null,
          "aa_length": 642,
          "cds_start": 1476,
          "cds_end": null,
          "cds_length": 1929,
          "cdna_start": 1743,
          "cdna_end": null,
          "cdna_length": 2387,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.741G>A",
          "hgvs_p": "p.Pro247Pro",
          "transcript": "ENST00000641820.1",
          "protein_id": "ENSP00000492937.1",
          "transcript_support_level": null,
          "aa_start": 247,
          "aa_end": null,
          "aa_length": 411,
          "cds_start": 741,
          "cds_end": null,
          "cds_length": 1236,
          "cdna_start": 1036,
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          "mane_select": null,
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        },
        {
          "aa_ref": "P",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 9,
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1599G>A",
          "hgvs_p": "p.Pro533Pro",
          "transcript": "XM_011541496.4",
          "protein_id": "XP_011539798.1",
          "transcript_support_level": null,
          "aa_start": 533,
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          "aa_length": 683,
          "cds_start": 1599,
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          "cdna_start": 1622,
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          "cdna_length": 6892,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "P",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 9,
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "MTHFR",
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          "hgvs_c": "c.1596G>A",
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          "transcript": "XM_047421174.1",
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        {
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          "protein_coding": true,
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          "gene_hgnc_id": 7436,
          "hgvs_c": "c.1476G>A",
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        {
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          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "MTHFR",
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          "hgvs_c": "c.1476G>A",
          "hgvs_p": "p.Pro492Pro",
          "transcript": "XM_047421178.1",
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        {
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        {
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          "gene_symbol": "MTHFR",
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        {
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        {
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        {
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          "gene_symbol": "MTHFR",
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        {
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          "intron_rank": null,
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          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.1476G>A",
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          "transcript": "ENST00000641446.1",
          "protein_id": "ENSP00000493262.1",
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          "feature": null
        },
        {
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          "canonical": false,
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          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 8,
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          "exon_count": 11,
          "intron_rank": null,
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          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.*988G>A",
          "hgvs_p": null,
          "transcript": "ENST00000641747.1",
          "protein_id": "ENSP00000493116.1",
          "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": 3227,
          "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": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.1845G>A",
          "hgvs_p": null,
          "transcript": "ENST00000641759.1",
          "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": 2454,
          "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": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.1993G>A",
          "hgvs_p": null,
          "transcript": "ENST00000641805.1",
          "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": 2945,
          "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": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MTHFR",
          "gene_hgnc_id": 7436,
          "hgvs_c": "n.*988G>A",
          "hgvs_p": null,
          "transcript": "ENST00000641747.1",
          "protein_id": "ENSP00000493116.1",
          "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": 3227,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "MTHFR",
      "gene_hgnc_id": 7436,
      "dbsnp": "rs35653697",
      "frequency_reference_population": 0.0017255951,
      "hom_count_reference_population": 41,
      "allele_count_reference_population": 2785,
      "gnomad_exomes_af": 0.00100234,
      "gnomad_genomes_af": 0.00866369,
      "gnomad_exomes_ac": 1465,
      "gnomad_genomes_ac": 1320,
      "gnomad_exomes_homalt": 16,
      "gnomad_genomes_homalt": 25,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.5699999928474426,
      "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": -0.57,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -3.348,
      "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": -21,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
      "acmg_by_gene": [
        {
          "score": -21,
          "benign_score": 21,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7",
            "BS1",
            "BS2"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000376590.9",
          "gene_symbol": "MTHFR",
          "hgnc_id": 7436,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1476G>A",
          "hgvs_p": "p.Pro492Pro"
        }
      ],
      "clinvar_disease": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency,Inborn genetic diseases,not provided,not specified",
      "clinvar_classification": "Benign/Likely benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "LB:2 B:3",
      "phenotype_combined": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency|not specified|Inborn genetic diseases|not provided",
      "pathogenicity_classification_combined": "Benign/Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}