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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: 1-43930190-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=43930190&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 43930190,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "ENST00000347631.8",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.1097G>A",
          "hgvs_p": "p.Arg366His",
          "transcript": "NM_006279.5",
          "protein_id": "NP_006270.1",
          "transcript_support_level": null,
          "aa_start": 366,
          "aa_end": null,
          "aa_length": 375,
          "cds_start": 1097,
          "cds_end": null,
          "cds_length": 1128,
          "cdna_start": 1285,
          "cdna_end": null,
          "cdna_length": 2254,
          "mane_select": "ENST00000347631.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.1097G>A",
          "hgvs_p": "p.Arg366His",
          "transcript": "ENST00000347631.8",
          "protein_id": "ENSP00000317192.6",
          "transcript_support_level": 5,
          "aa_start": 366,
          "aa_end": null,
          "aa_length": 375,
          "cds_start": 1097,
          "cds_end": null,
          "cds_length": 1128,
          "cdna_start": 1285,
          "cdna_end": null,
          "cdna_length": 2254,
          "mane_select": "NM_006279.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.1211G>A",
          "hgvs_p": "p.Arg404His",
          "transcript": "ENST00000372372.7",
          "protein_id": "ENSP00000361447.2",
          "transcript_support_level": 1,
          "aa_start": 404,
          "aa_end": null,
          "aa_length": 413,
          "cds_start": 1211,
          "cds_end": null,
          "cds_length": 1242,
          "cdna_start": 1408,
          "cdna_end": null,
          "cdna_length": 2109,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.1190G>A",
          "hgvs_p": "p.Arg397His",
          "transcript": "ENST00000361746.9",
          "protein_id": "ENSP00000354657.5",
          "transcript_support_level": 1,
          "aa_start": 397,
          "aa_end": null,
          "aa_length": 406,
          "cds_start": 1190,
          "cds_end": null,
          "cds_length": 1221,
          "cdna_start": 1267,
          "cdna_end": null,
          "cdna_length": 2229,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.1142G>A",
          "hgvs_p": "p.Arg381His",
          "transcript": "ENST00000361392.9",
          "protein_id": "ENSP00000355341.5",
          "transcript_support_level": 1,
          "aa_start": 381,
          "aa_end": null,
          "aa_length": 390,
          "cds_start": 1142,
          "cds_end": null,
          "cds_length": 1173,
          "cdna_start": 1328,
          "cdna_end": null,
          "cdna_length": 2297,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.1112G>A",
          "hgvs_p": "p.Arg371His",
          "transcript": "ENST00000372368.7",
          "protein_id": "ENSP00000361443.3",
          "transcript_support_level": 1,
          "aa_start": 371,
          "aa_end": null,
          "aa_length": 380,
          "cds_start": 1112,
          "cds_end": null,
          "cds_length": 1143,
          "cdna_start": 1142,
          "cdna_end": null,
          "cdna_length": 2074,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.1049G>A",
          "hgvs_p": "p.Arg350His",
          "transcript": "ENST00000361400.9",
          "protein_id": "ENSP00000354748.4",
          "transcript_support_level": 1,
          "aa_start": 350,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 1049,
          "cds_end": null,
          "cds_length": 1080,
          "cdna_start": 1240,
          "cdna_end": null,
          "cdna_length": 2212,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.1007G>A",
          "hgvs_p": "p.Arg336His",
          "transcript": "ENST00000372369.5",
          "protein_id": "ENSP00000361444.1",
          "transcript_support_level": 1,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 345,
          "cds_start": 1007,
          "cds_end": null,
          "cds_length": 1038,
          "cdna_start": 1007,
          "cdna_end": null,
          "cdna_length": 1038,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.893G>A",
          "hgvs_p": "p.Arg298His",
          "transcript": "ENST00000533933.6",
          "protein_id": "ENSP00000432965.2",
          "transcript_support_level": 1,
          "aa_start": 298,
          "aa_end": null,
          "aa_length": 307,
          "cds_start": 893,
          "cds_end": null,
          "cds_length": 924,
          "cdna_start": 893,
          "cdna_end": null,
          "cdna_length": 1844,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.881G>A",
          "hgvs_p": "p.Arg294His",
          "transcript": "ENST00000332628.11",
          "protein_id": "ENSP00000329755.7",
          "transcript_support_level": 1,
          "aa_start": 294,
          "aa_end": null,
          "aa_length": 303,
          "cds_start": 881,
          "cds_end": null,
          "cds_length": 912,
          "cdna_start": 883,
          "cdna_end": null,
          "cdna_length": 1681,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "R",
          "aa_alt": "H",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.662G>A",
          "hgvs_p": "p.Arg221His",
          "transcript": "ENST00000531993.6",
          "protein_id": "ENSP00000432682.2",
          "transcript_support_level": 1,
          "aa_start": 221,
          "aa_end": null,
          "aa_length": 230,
          "cds_start": 662,
          "cds_end": null,
          "cds_length": 693,
          "cdna_start": 662,
          "cdna_end": null,
          "cdna_length": 693,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.501G>A",
          "hgvs_p": "p.Ser167Ser",
          "transcript": "ENST00000361812.9",
          "protein_id": "ENSP00000355201.4",
          "transcript_support_level": 1,
          "aa_start": 167,
          "aa_end": null,
          "aa_length": 170,
          "cds_start": 501,
          "cds_end": null,
          "cds_length": 513,
          "cdna_start": 501,
          "cdna_end": null,
          "cdna_length": 1020,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.456G>A",
          "hgvs_p": "p.Ser152Ser",
          "transcript": "ENST00000372362.6",
          "protein_id": "ENSP00000361437.2",
          "transcript_support_level": 1,
          "aa_start": 152,
          "aa_end": null,
          "aa_length": 155,
          "cds_start": 456,
          "cds_end": null,
          "cds_length": 468,
          "cdna_start": 456,
          "cdna_end": null,
          "cdna_length": 468,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "S",
          "aa_alt": "S",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "c.408G>A",
          "hgvs_p": "p.Ser136Ser",
          "transcript": "ENST00000531451.5",
          "protein_id": "ENSP00000435603.1",
          "transcript_support_level": 1,
          "aa_start": 136,
          "aa_end": null,
          "aa_length": 139,
          "cds_start": 408,
          "cds_end": null,
          "cds_length": 420,
          "cdna_start": 408,
          "cdna_end": null,
          "cdna_length": 420,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "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": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "n.*723G>A",
          "hgvs_p": null,
          "transcript": "ENST00000469715.6",
          "protein_id": "ENSP00000431700.2",
          "transcript_support_level": 1,
          "aa_start": null,
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          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 1277,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "n.*874G>A",
          "hgvs_p": null,
          "transcript": "ENST00000490541.6",
          "protein_id": "ENSP00000435018.2",
          "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,
          "cdna_end": null,
          "cdna_length": 1037,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 9,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "n.*175G>A",
          "hgvs_p": null,
          "transcript": "ENST00000530581.5",
          "protein_id": "ENSP00000437293.1",
          "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,
          "cdna_end": null,
          "cdna_length": 893,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "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": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "n.*294G>A",
          "hgvs_p": null,
          "transcript": "ENST00000533212.5",
          "protein_id": "ENSP00000435621.1",
          "transcript_support_level": 1,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 781,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
          "hgvs_c": "n.*628G>A",
          "hgvs_p": null,
          "transcript": "ENST00000533997.6",
          "protein_id": "ENSP00000432071.1",
          "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,
          "cdna_end": null,
          "cdna_length": 1191,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 26,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000284989",
          "gene_hgnc_id": null,
          "hgvs_c": "n.*2419G>A",
          "hgvs_p": null,
          "transcript": "ENST00000645057.1",
          "protein_id": "ENSP00000494063.1",
          "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": 4037,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ST3GAL3",
          "gene_hgnc_id": 10866,
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      "gnomad_exomes_homalt": 1,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
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      "computational_score_selected": 0.05643525719642639,
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      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
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      "revel_prediction": "Benign",
      "alphamissense_score": 0.0878,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.44,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.04,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
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      "acmg_score": -5,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Strong,BS1_Supporting",
      "acmg_by_gene": [
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            "BS1_Supporting"
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          "verdict": "Likely_benign",
          "transcript": "ENST00000347631.8",
          "gene_symbol": "ST3GAL3",
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        {
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          "verdict": "Likely_benign",
          "transcript": "ENST00000645057.1",
          "gene_symbol": "ENSG00000284989",
          "hgnc_id": null,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.*2419G>A",
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      "clinvar_disease": "Developmental and epileptic encephalopathy,Inborn genetic diseases,not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "US:3",
      "phenotype_combined": "not specified|Developmental and epileptic encephalopathy|Inborn genetic diseases",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}