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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: X-150619036-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=150619036&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "X",
      "pos": 150619036,
      "ref": "A",
      "alt": "G",
      "effect": "splice_acceptor_variant,intron_variant",
      "transcript": "NM_000252.3",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "NM_000252.3",
          "protein_id": "NP_000243.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000370396.7",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_000252.3"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000370396.7",
          "protein_id": "ENSP00000359423.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_000252.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000370396.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.388-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000689314.1",
          "protein_id": "ENSP00000510607.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 618,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1857,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000689314.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.388-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866458.1",
          "protein_id": "ENSP00000536517.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 618,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1857,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866458.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "NM_001376908.1",
          "protein_id": "NP_001363837.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001376908.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000685944.1",
          "protein_id": "ENSP00000509266.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000685944.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000689694.1",
          "protein_id": "ENSP00000508718.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000689694.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866460.1",
          "protein_id": "ENSP00000536519.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866460.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866461.1",
          "protein_id": "ENSP00000536520.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866461.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866462.1",
          "protein_id": "ENSP00000536521.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866462.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866463.1",
          "protein_id": "ENSP00000536522.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866463.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866464.1",
          "protein_id": "ENSP00000536523.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866464.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866466.1",
          "protein_id": "ENSP00000536525.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866466.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866467.1",
          "protein_id": "ENSP00000536526.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866467.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": 7,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866468.1",
          "protein_id": "ENSP00000536527.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866468.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866469.1",
          "protein_id": "ENSP00000536528.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866469.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": 6,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866470.1",
          "protein_id": "ENSP00000536529.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
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          "cds_length": 1812,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866470.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866473.1",
          "protein_id": "ENSP00000536532.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 603,
          "cds_start": null,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866473.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866474.1",
          "protein_id": "ENSP00000536533.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 603,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1812,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000866474.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "splice_acceptor_variant",
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": 5,
          "intron_rank_end": null,
          "gene_symbol": "MTM1",
          "gene_hgnc_id": 7448,
          "hgvs_c": "c.343-2A>G",
          "hgvs_p": null,
          "transcript": "ENST00000866475.1",
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      "gene_symbol": "MTM1",
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      "dbsnp": "rs587783821",
      "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": 0.3100000023841858,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0.9279999732971191,
      "splice_prediction_selected": "Pathogenic",
      "splice_source_selected": "dbscSNV1_RF",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.31,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 8.845,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0.86,
      "spliceai_max_prediction": "Pathogenic",
      "dbscsnv_ada_score": 0.999993519952936,
      "dbscsnv_ada_prediction": "Pathogenic",
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 6,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
      "acmg_by_gene": [
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PVS1_Moderate",
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_000252.3",
          "gene_symbol": "MTM1",
          "hgnc_id": 7448,
          "effects": [
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          "inheritance_mode": "XL",
          "hgvs_c": "c.343-2A>G",
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      ],
      "clinvar_disease": "Severe X-linked myotubular myopathy",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "P:1",
      "phenotype_combined": "Severe X-linked myotubular myopathy",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}