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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: 11-47438029-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=47438029&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "11",
      "pos": 47438029,
      "ref": "C",
      "alt": "T",
      "effect": "missense_variant",
      "transcript": "NM_001440490.1",
      "consequences": [
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "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": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1185G>A",
          "hgvs_p": "p.Gly395Gly",
          "transcript": "NM_005055.5",
          "protein_id": "NP_005046.2",
          "transcript_support_level": null,
          "aa_start": 395,
          "aa_end": null,
          "aa_length": 412,
          "cds_start": 1185,
          "cds_end": null,
          "cds_length": 1239,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000298854.7",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_005055.5"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "canonical": true,
          "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": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1185G>A",
          "hgvs_p": "p.Gly395Gly",
          "transcript": "ENST00000298854.7",
          "protein_id": "ENSP00000298854.2",
          "transcript_support_level": 1,
          "aa_start": 395,
          "aa_end": null,
          "aa_length": 412,
          "cds_start": 1185,
          "cds_end": null,
          "cds_length": 1239,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_005055.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000298854.7"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "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": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1008G>A",
          "hgvs_p": "p.Gly336Gly",
          "transcript": "ENST00000352508.7",
          "protein_id": "ENSP00000298853.3",
          "transcript_support_level": 1,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 353,
          "cds_start": 1008,
          "cds_end": null,
          "cds_length": 1062,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000352508.7"
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1321G>A",
          "hgvs_p": "p.Asp441Asn",
          "transcript": "NM_001440490.1",
          "protein_id": "NP_001427419.1",
          "transcript_support_level": null,
          "aa_start": 441,
          "aa_end": null,
          "aa_length": 520,
          "cds_start": 1321,
          "cds_end": null,
          "cds_length": 1563,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440490.1"
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 8,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1270G>A",
          "hgvs_p": "p.Asp424Asn",
          "transcript": "NM_001440491.1",
          "protein_id": "NP_001427420.1",
          "transcript_support_level": null,
          "aa_start": 424,
          "aa_end": null,
          "aa_length": 503,
          "cds_start": 1270,
          "cds_end": null,
          "cds_length": 1512,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440491.1"
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.988G>A",
          "hgvs_p": "p.Asp330Asn",
          "transcript": "NM_001440493.1",
          "protein_id": "NP_001427422.1",
          "transcript_support_level": null,
          "aa_start": 330,
          "aa_end": null,
          "aa_length": 409,
          "cds_start": 988,
          "cds_end": null,
          "cds_length": 1230,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440493.1"
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.985G>A",
          "hgvs_p": "p.Asp329Asn",
          "transcript": "NM_001440494.1",
          "protein_id": "NP_001427423.1",
          "transcript_support_level": null,
          "aa_start": 329,
          "aa_end": null,
          "aa_length": 408,
          "cds_start": 985,
          "cds_end": null,
          "cds_length": 1227,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440494.1"
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.931G>A",
          "hgvs_p": "p.Asp311Asn",
          "transcript": "NM_001440496.1",
          "protein_id": "NP_001427425.1",
          "transcript_support_level": null,
          "aa_start": 311,
          "aa_end": null,
          "aa_length": 390,
          "cds_start": 931,
          "cds_end": null,
          "cds_length": 1173,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440496.1"
        },
        {
          "aa_ref": "D",
          "aa_alt": "N",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.808G>A",
          "hgvs_p": "p.Asp270Asn",
          "transcript": "NM_001440501.1",
          "protein_id": "NP_001427430.1",
          "transcript_support_level": null,
          "aa_start": 270,
          "aa_end": null,
          "aa_length": 349,
          "cds_start": 808,
          "cds_end": null,
          "cds_length": 1050,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440501.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "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": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1176G>A",
          "hgvs_p": "p.Gly392Gly",
          "transcript": "ENST00000949301.1",
          "protein_id": "ENSP00000619360.1",
          "transcript_support_level": null,
          "aa_start": 392,
          "aa_end": null,
          "aa_length": 409,
          "cds_start": 1176,
          "cds_end": null,
          "cds_length": 1230,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000949301.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "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": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1173G>A",
          "hgvs_p": "p.Gly391Gly",
          "transcript": "ENST00000949304.1",
          "protein_id": "ENSP00000619363.1",
          "transcript_support_level": null,
          "aa_start": 391,
          "aa_end": null,
          "aa_length": 408,
          "cds_start": 1173,
          "cds_end": null,
          "cds_length": 1227,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000949304.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1131G>A",
          "hgvs_p": "p.Gly377Gly",
          "transcript": "NM_001440495.1",
          "protein_id": "NP_001427424.1",
          "transcript_support_level": null,
          "aa_start": 377,
          "aa_end": null,
          "aa_length": 394,
          "cds_start": 1131,
          "cds_end": null,
          "cds_length": 1185,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440495.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1131G>A",
          "hgvs_p": "p.Gly377Gly",
          "transcript": "ENST00000897203.1",
          "protein_id": "ENSP00000567262.1",
          "transcript_support_level": null,
          "aa_start": 377,
          "aa_end": null,
          "aa_length": 394,
          "cds_start": 1131,
          "cds_end": null,
          "cds_length": 1185,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000897203.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1062G>A",
          "hgvs_p": "p.Gly354Gly",
          "transcript": "NM_001440497.1",
          "protein_id": "NP_001427426.1",
          "transcript_support_level": null,
          "aa_start": 354,
          "aa_end": null,
          "aa_length": 371,
          "cds_start": 1062,
          "cds_end": null,
          "cds_length": 1116,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440497.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1062G>A",
          "hgvs_p": "p.Gly354Gly",
          "transcript": "ENST00000897204.1",
          "protein_id": "ENSP00000567263.1",
          "transcript_support_level": null,
          "aa_start": 354,
          "aa_end": null,
          "aa_length": 371,
          "cds_start": 1062,
          "cds_end": null,
          "cds_length": 1116,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000897204.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1026G>A",
          "hgvs_p": "p.Gly342Gly",
          "transcript": "NM_001440499.1",
          "protein_id": "NP_001427428.1",
          "transcript_support_level": null,
          "aa_start": 342,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 1026,
          "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_001440499.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1026G>A",
          "hgvs_p": "p.Gly342Gly",
          "transcript": "ENST00000524487.5",
          "protein_id": "ENSP00000435551.2",
          "transcript_support_level": 5,
          "aa_start": 342,
          "aa_end": null,
          "aa_length": 359,
          "cds_start": 1026,
          "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": "ENST00000524487.5"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "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": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.1008G>A",
          "hgvs_p": "p.Gly336Gly",
          "transcript": "NM_032645.5",
          "protein_id": "NP_116034.2",
          "transcript_support_level": null,
          "aa_start": 336,
          "aa_end": null,
          "aa_length": 353,
          "cds_start": 1008,
          "cds_end": null,
          "cds_length": 1062,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_032645.5"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "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": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.972G>A",
          "hgvs_p": "p.Gly324Gly",
          "transcript": "NM_001440502.1",
          "protein_id": "NP_001427431.1",
          "transcript_support_level": null,
          "aa_start": 324,
          "aa_end": null,
          "aa_length": 341,
          "cds_start": 972,
          "cds_end": null,
          "cds_length": 1026,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001440502.1"
        },
        {
          "aa_ref": "G",
          "aa_alt": "G",
          "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": "RAPSN",
          "gene_hgnc_id": 9863,
          "hgvs_c": "c.972G>A",
          "hgvs_p": "p.Gly324Gly",
          "transcript": "ENST00000949303.1",
          "protein_id": "ENSP00000619362.1",
          "transcript_support_level": null,
          "aa_start": 324,
          "aa_end": null,
          "aa_length": 341,
          "cds_start": 972,
          "cds_end": null,
          "cds_length": 1026,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000949303.1"
        },
        {
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          "biotype": "pseudogene",
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      ],
      "gene_symbol": "RAPSN",
      "gene_hgnc_id": 9863,
      "dbsnp": "rs1287446389",
      "frequency_reference_population": 0.0000014309632,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": 0.00000143096,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 2,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.28700000047683716,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "REVEL",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.287,
      "revel_prediction": "Benign",
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.38,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.334,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.01,
      "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": -1,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PM2,BP4,BP6_Moderate",
      "acmg_by_gene": [
        {
          "score": -1,
          "benign_score": 3,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4",
            "BP6_Moderate"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_001440490.1",
          "gene_symbol": "RAPSN",
          "hgnc_id": 9863,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.1321G>A",
          "hgvs_p": "p.Asp441Asn"
        },
        {
          "score": -1,
          "benign_score": 3,
          "pathogenic_score": 2,
          "criteria": [
            "PM2",
            "BP4",
            "BP6_Moderate"
          ],
          "verdict": "Likely_benign",
          "transcript": "XR_007062669.1",
          "gene_symbol": "LOC124902673",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.144+262C>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Congenital myasthenic syndrome 11,Fetal akinesia deformation sequence 1",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "LB:1",
      "phenotype_combined": "Congenital myasthenic syndrome 11;Fetal akinesia deformation sequence 1",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}