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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: 2-178590480-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=178590480&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 178590480,
      "ref": "T",
      "alt": "C",
      "effect": "synonymous_variant",
      "transcript": "ENST00000589042.5",
      "consequences": [
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 304,
          "exon_rank_end": null,
          "exon_count": 363,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.61245A>G",
          "hgvs_p": "p.Thr20415Thr",
          "transcript": "NM_001267550.2",
          "protein_id": "NP_001254479.2",
          "transcript_support_level": null,
          "aa_start": 20415,
          "aa_end": null,
          "aa_length": 35991,
          "cds_start": 61245,
          "cds_end": null,
          "cds_length": 107976,
          "cdna_start": 61470,
          "cdna_end": null,
          "cdna_length": 109224,
          "mane_select": "ENST00000589042.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 304,
          "exon_rank_end": null,
          "exon_count": 363,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.61245A>G",
          "hgvs_p": "p.Thr20415Thr",
          "transcript": "ENST00000589042.5",
          "protein_id": "ENSP00000467141.1",
          "transcript_support_level": 5,
          "aa_start": 20415,
          "aa_end": null,
          "aa_length": 35991,
          "cds_start": 61245,
          "cds_end": null,
          "cds_length": 107976,
          "cdna_start": 61470,
          "cdna_end": null,
          "cdna_length": 109224,
          "mane_select": "NM_001267550.2",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 302,
          "exon_rank_end": null,
          "exon_count": 361,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.61089A>G",
          "hgvs_p": "p.Thr20363Thr",
          "transcript": "ENST00000446966.2",
          "protein_id": "ENSP00000408004.2",
          "transcript_support_level": 1,
          "aa_start": 20363,
          "aa_end": null,
          "aa_length": 35939,
          "cds_start": 61089,
          "cds_end": null,
          "cds_length": 107820,
          "cdna_start": 61314,
          "cdna_end": null,
          "cdna_length": 109068,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 302,
          "exon_rank_end": null,
          "exon_count": 361,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.60969A>G",
          "hgvs_p": "p.Thr20323Thr",
          "transcript": "ENST00000436599.2",
          "protein_id": "ENSP00000405517.2",
          "transcript_support_level": 1,
          "aa_start": 20323,
          "aa_end": null,
          "aa_length": 35899,
          "cds_start": 60969,
          "cds_end": null,
          "cds_length": 107700,
          "cdna_start": 61194,
          "cdna_end": null,
          "cdna_length": 108948,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 297,
          "exon_rank_end": null,
          "exon_count": 356,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.60687A>G",
          "hgvs_p": "p.Thr20229Thr",
          "transcript": "ENST00000426232.6",
          "protein_id": "ENSP00000392336.2",
          "transcript_support_level": 1,
          "aa_start": 20229,
          "aa_end": null,
          "aa_length": 35805,
          "cds_start": 60687,
          "cds_end": null,
          "cds_length": 107418,
          "cdna_start": 60912,
          "cdna_end": null,
          "cdna_length": 108666,
          "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": 17,
          "intron_rank": 11,
          "intron_rank_end": null,
          "gene_symbol": "TTN-AS1",
          "gene_hgnc_id": 44124,
          "hgvs_c": "n.3189-659T>C",
          "hgvs_p": null,
          "transcript": "ENST00000419746.5",
          "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,
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          "cdna_length": 4592,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 306,
          "exon_rank_end": null,
          "exon_count": 365,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.61245A>G",
          "hgvs_p": "p.Thr20415Thr",
          "transcript": "ENST00000412264.2",
          "protein_id": "ENSP00000394672.2",
          "transcript_support_level": 3,
          "aa_start": 20415,
          "aa_end": null,
          "aa_length": 35991,
          "cds_start": 61245,
          "cds_end": null,
          "cds_length": 107976,
          "cdna_start": 61734,
          "cdna_end": null,
          "cdna_length": 109488,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 303,
          "exon_rank_end": null,
          "exon_count": 362,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.61161A>G",
          "hgvs_p": "p.Thr20387Thr",
          "transcript": "ENST00000425332.3",
          "protein_id": "ENSP00000396805.3",
          "transcript_support_level": 5,
          "aa_start": 20387,
          "aa_end": null,
          "aa_length": 35963,
          "cds_start": 61161,
          "cds_end": null,
          "cds_length": 107892,
          "cdna_start": 61386,
          "cdna_end": null,
          "cdna_length": 109140,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "T",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 301,
          "exon_rank_end": null,
          "exon_count": 360,
          "intron_rank": null,
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          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.60831A>G",
          "hgvs_p": "p.Thr20277Thr",
          "transcript": "ENST00000715174.1",
          "protein_id": "ENSP00000520370.1",
          "transcript_support_level": null,
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          "cds_start": 60831,
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        {
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          "consequences": [
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          "exon_rank": 254,
          "exon_rank_end": null,
          "exon_count": 313,
          "intron_rank": null,
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          "gene_symbol": "TTN",
          "gene_hgnc_id": 12403,
          "hgvs_c": "c.56322A>G",
          "hgvs_p": "p.Thr18774Thr",
          "transcript": "NM_001256850.1",
          "protein_id": "NP_001243779.1",
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        {
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          "gene_symbol": "TTN",
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        {
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          "gene_symbol": "TTN-AS1",
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          "hgvs_c": "n.421-7116T>C",
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          "cdna_length": 1069,
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        },
        {
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          ],
          "exon_rank": null,
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          "exon_count": 7,
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          "gene_symbol": "TTN-AS1",
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          "hgvs_c": "n.597-7116T>C",
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          "transcript": "NR_038271.1",
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        },
        {
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          "exon_count": 17,
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          "intron_rank_end": null,
          "gene_symbol": "TTN-AS1",
          "gene_hgnc_id": 44124,
          "hgvs_c": "n.3189-659T>C",
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          "transcript": "NR_038272.1",
          "protein_id": null,
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          "cdna_length": 4592,
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        }
      ],
      "gene_symbol": "TTN",
      "gene_hgnc_id": 12403,
      "dbsnp": "rs2163009",
      "frequency_reference_population": 0.2790011,
      "hom_count_reference_population": 75669,
      "allele_count_reference_population": 449935,
      "gnomad_exomes_af": 0.270231,
      "gnomad_genomes_af": 0.363384,
      "gnomad_exomes_ac": 394761,
      "gnomad_genomes_ac": 55174,
      "gnomad_exomes_homalt": 63759,
      "gnomad_genomes_homalt": 11910,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.8600000143051147,
      "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": -0.86,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.266,
      "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,BA1",
      "acmg_by_gene": [
        {
          "score": -21,
          "benign_score": 21,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BP7",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000589042.5",
          "gene_symbol": "TTN",
          "hgnc_id": 12403,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.61245A>G",
          "hgvs_p": "p.Thr20415Thr"
        },
        {
          "score": -20,
          "benign_score": 20,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6_Very_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000419746.5",
          "gene_symbol": "TTN-AS1",
          "hgnc_id": 44124,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.3189-659T>C",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " 9, myofibrillar, with early respiratory failure,Autosomal recessive limb-girdle muscular dystrophy type 2J,Cardiovascular phenotype,Dilated cardiomyopathy 1G,Early-onset myopathy with fatal cardiomyopathy,Myopathy,Tibial muscular dystrophy,not provided,not specified",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "B:19",
      "phenotype_combined": "not specified|Dilated cardiomyopathy 1G|Cardiovascular phenotype|Myopathy, myofibrillar, 9, with early respiratory failure|Autosomal recessive limb-girdle muscular dystrophy type 2J|Tibial muscular dystrophy|not provided|Early-onset myopathy with fatal cardiomyopathy|Autosomal recessive limb-girdle muscular dystrophy type 2J;Dilated cardiomyopathy 1G",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}