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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: 3-49417546-G-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49417546&ref=G&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 49417546,
      "ref": "G",
      "alt": "C",
      "effect": "synonymous_variant",
      "transcript": "NM_000481.4",
      "consequences": [
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1206C>G",
          "hgvs_p": "p.Leu402Leu",
          "transcript": "NM_000481.4",
          "protein_id": "NP_000472.2",
          "transcript_support_level": null,
          "aa_start": 402,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 1206,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000273588.9",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_000481.4"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1206C>G",
          "hgvs_p": "p.Leu402Leu",
          "transcript": "ENST00000273588.9",
          "protein_id": "ENSP00000273588.3",
          "transcript_support_level": 1,
          "aa_start": 402,
          "aa_end": null,
          "aa_length": 403,
          "cds_start": 1206,
          "cds_end": null,
          "cds_length": 1212,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_000481.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000273588.9"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000283189",
          "gene_hgnc_id": null,
          "hgvs_c": "c.1443C>G",
          "hgvs_p": "p.Leu481Leu",
          "transcript": "ENST00000636166.1",
          "protein_id": "ENSP00000490106.1",
          "transcript_support_level": 5,
          "aa_start": 481,
          "aa_end": null,
          "aa_length": 482,
          "cds_start": 1443,
          "cds_end": null,
          "cds_length": 1449,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000636166.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 9,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1137+69C>G",
          "hgvs_p": null,
          "transcript": "ENST00000395338.7",
          "protein_id": "ENSP00000378747.2",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 386,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1161,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000395338.7"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1125C>G",
          "hgvs_p": "p.Leu375Leu",
          "transcript": "ENST00000638063.1",
          "protein_id": "ENSP00000489760.1",
          "transcript_support_level": 5,
          "aa_start": 375,
          "aa_end": null,
          "aa_length": 376,
          "cds_start": 1125,
          "cds_end": null,
          "cds_length": 1131,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000638063.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1074C>G",
          "hgvs_p": "p.Leu358Leu",
          "transcript": "NM_001164710.2",
          "protein_id": "NP_001158182.1",
          "transcript_support_level": null,
          "aa_start": 358,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 1074,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001164710.2"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1074C>G",
          "hgvs_p": "p.Leu358Leu",
          "transcript": "ENST00000458307.6",
          "protein_id": "ENSP00000415619.2",
          "transcript_support_level": 2,
          "aa_start": 358,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 1074,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000458307.6"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1062C>G",
          "hgvs_p": "p.Leu354Leu",
          "transcript": "ENST00000538581.6",
          "protein_id": "ENSP00000443200.2",
          "transcript_support_level": 2,
          "aa_start": 354,
          "aa_end": null,
          "aa_length": 355,
          "cds_start": 1062,
          "cds_end": null,
          "cds_length": 1068,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000538581.6"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1050C>G",
          "hgvs_p": "p.Leu350Leu",
          "transcript": "ENST00000636865.1",
          "protein_id": "ENSP00000490601.1",
          "transcript_support_level": 5,
          "aa_start": 350,
          "aa_end": null,
          "aa_length": 351,
          "cds_start": 1050,
          "cds_end": null,
          "cds_length": 1056,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000636865.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1050C>G",
          "hgvs_p": "p.Leu350Leu",
          "transcript": "ENST00000637682.1",
          "protein_id": "ENSP00000489856.1",
          "transcript_support_level": 5,
          "aa_start": 350,
          "aa_end": null,
          "aa_length": 351,
          "cds_start": 1050,
          "cds_end": null,
          "cds_length": 1056,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000637682.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1038C>G",
          "hgvs_p": "p.Leu346Leu",
          "transcript": "NM_001164711.2",
          "protein_id": "NP_001158183.1",
          "transcript_support_level": null,
          "aa_start": 346,
          "aa_end": null,
          "aa_length": 347,
          "cds_start": 1038,
          "cds_end": null,
          "cds_length": 1044,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001164711.2"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1038C>G",
          "hgvs_p": "p.Leu346Leu",
          "transcript": "ENST00000636522.1",
          "protein_id": "ENSP00000489758.1",
          "transcript_support_level": 2,
          "aa_start": 346,
          "aa_end": null,
          "aa_length": 347,
          "cds_start": 1038,
          "cds_end": null,
          "cds_length": 1044,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000636522.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.768C>G",
          "hgvs_p": "p.Leu256Leu",
          "transcript": "ENST00000636199.1",
          "protein_id": "ENSP00000490871.1",
          "transcript_support_level": 5,
          "aa_start": 256,
          "aa_end": null,
          "aa_length": 257,
          "cds_start": 768,
          "cds_end": null,
          "cds_length": 774,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000636199.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.723C>G",
          "hgvs_p": "p.Leu241Leu",
          "transcript": "ENST00000636597.1",
          "protein_id": "ENSP00000490251.1",
          "transcript_support_level": 5,
          "aa_start": 241,
          "aa_end": null,
          "aa_length": 242,
          "cds_start": 723,
          "cds_end": null,
          "cds_length": 729,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000636597.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 9,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1137+69C>G",
          "hgvs_p": null,
          "transcript": "NM_001164712.2",
          "protein_id": "NP_001158184.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 386,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1161,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001164712.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": 8,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.1056+69C>G",
          "hgvs_p": null,
          "transcript": "ENST00000635808.1",
          "protein_id": "ENSP00000489620.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000635808.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 9,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.993+69C>G",
          "hgvs_p": null,
          "transcript": "ENST00000427987.6",
          "protein_id": "ENSP00000403821.2",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 338,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1017,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000427987.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": 8,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.948+69C>G",
          "hgvs_p": null,
          "transcript": "ENST00000637455.1",
          "protein_id": "ENSP00000489628.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 321,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 966,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000637455.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "c.315+69C>G",
          "hgvs_p": null,
          "transcript": "ENST00000636188.1",
          "protein_id": "ENSP00000490324.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 145,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 438,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000636188.1"
        },
        {
          "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": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "AMT",
          "gene_hgnc_id": 473,
          "hgvs_c": "n.*578C>G",
          "hgvs_p": null,
          "transcript": "ENST00000399379.7",
          "protein_id": "ENSP00000399943.2",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000399379.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
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        {
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          "hgvs_c": "n.1249+69C>G",
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          "feature": "ENST00000636978.1"
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      ],
      "gene_symbol": "AMT",
      "gene_hgnc_id": 473,
      "dbsnp": "rs2107928357",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.8100000023841858,
      "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": -0.81,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.19,
      "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": -5,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
      "acmg_by_gene": [
        {
          "score": -5,
          "benign_score": 7,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong",
            "BP6_Moderate",
            "BP7"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_000481.4",
          "gene_symbol": "AMT",
          "hgnc_id": 473,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR,Unknown",
          "hgvs_c": "c.1206C>G",
          "hgvs_p": "p.Leu402Leu"
        },
        {
          "score": -5,
          "benign_score": 7,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4_Strong",
            "BP6_Moderate",
            "BP7"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000636166.1",
          "gene_symbol": "ENSG00000283189",
          "hgnc_id": null,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.1443C>G",
          "hgvs_p": "p.Leu481Leu"
        }
      ],
      "clinvar_disease": "Glycine encephalopathy",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LB:1",
      "phenotype_combined": "Glycine encephalopathy",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}