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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: 9-36220003-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=36220003&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 36220003,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005476.7",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1744A>G",
"hgvs_p": "p.Ile582Val",
"transcript": "NM_001128227.3",
"protein_id": "NP_001121699.1",
"transcript_support_level": null,
"aa_start": 582,
"aa_end": null,
"aa_length": 753,
"cds_start": 1744,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 1778,
"cdna_end": null,
"cdna_length": 5220,
"mane_select": null,
"mane_plus": "ENST00000396594.8",
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1744A>G",
"hgvs_p": "p.Ile582Val",
"transcript": "ENST00000396594.8",
"protein_id": "ENSP00000379839.3",
"transcript_support_level": 1,
"aa_start": 582,
"aa_end": null,
"aa_length": 753,
"cds_start": 1744,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 1778,
"cdna_end": null,
"cdna_length": 5220,
"mane_select": null,
"mane_plus": "NM_001128227.3",
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1651A>G",
"hgvs_p": "p.Ile551Val",
"transcript": "NM_005476.7",
"protein_id": "NP_005467.1",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 722,
"cds_start": 1651,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 1821,
"cdna_end": null,
"cdna_length": 5263,
"mane_select": "ENST00000642385.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1651A>G",
"hgvs_p": "p.Ile551Val",
"transcript": "ENST00000642385.2",
"protein_id": "ENSP00000494141.2",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 722,
"cds_start": 1651,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 1821,
"cdna_end": null,
"cdna_length": 5263,
"mane_select": "NM_005476.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1474A>G",
"hgvs_p": "p.Ile492Val",
"transcript": "ENST00000543356.7",
"protein_id": "ENSP00000437765.3",
"transcript_support_level": 1,
"aa_start": 492,
"aa_end": null,
"aa_length": 663,
"cds_start": 1474,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 1636,
"cdna_end": null,
"cdna_length": 2576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1498A>G",
"hgvs_p": "p.Ile500Val",
"transcript": "NM_001374797.1",
"protein_id": "NP_001361726.1",
"transcript_support_level": null,
"aa_start": 500,
"aa_end": null,
"aa_length": 671,
"cds_start": 1498,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1668,
"cdna_end": null,
"cdna_length": 5110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1474A>G",
"hgvs_p": "p.Ile492Val",
"transcript": "NM_001190388.2",
"protein_id": "NP_001177317.2",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 663,
"cds_start": 1474,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 1572,
"cdna_end": null,
"cdna_length": 5014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1474A>G",
"hgvs_p": "p.Ile492Val",
"transcript": "NM_001374798.1",
"protein_id": "NP_001361727.1",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 663,
"cds_start": 1474,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 1615,
"cdna_end": null,
"cdna_length": 5057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1429A>G",
"hgvs_p": "p.Ile477Val",
"transcript": "NM_001190383.3",
"protein_id": "NP_001177312.1",
"transcript_support_level": null,
"aa_start": 477,
"aa_end": null,
"aa_length": 648,
"cds_start": 1429,
"cds_end": null,
"cds_length": 1947,
"cdna_start": 1599,
"cdna_end": null,
"cdna_length": 5041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1429A>G",
"hgvs_p": "p.Ile477Val",
"transcript": "ENST00000447283.6",
"protein_id": "ENSP00000414760.2",
"transcript_support_level": 5,
"aa_start": 477,
"aa_end": null,
"aa_length": 648,
"cds_start": 1429,
"cds_end": null,
"cds_length": 1947,
"cdna_start": 1480,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1321A>G",
"hgvs_p": "p.Ile441Val",
"transcript": "NM_001190384.3",
"protein_id": "NP_001177313.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 612,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1462,
"cdna_end": null,
"cdna_length": 4904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1321A>G",
"hgvs_p": "p.Ile441Val",
"transcript": "ENST00000539208.5",
"protein_id": "ENSP00000445117.1",
"transcript_support_level": 2,
"aa_start": 441,
"aa_end": null,
"aa_length": 612,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1459,
"cdna_end": null,
"cdna_length": 2190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1651A>G",
"hgvs_p": "p.Ile551Val",
"transcript": "XM_017014167.1",
"protein_id": "XP_016869656.1",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 722,
"cds_start": 1651,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 1717,
"cdna_end": null,
"cdna_length": 5159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1591A>G",
"hgvs_p": "p.Ile531Val",
"transcript": "XM_005251334.5",
"protein_id": "XP_005251391.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 702,
"cds_start": 1591,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1625,
"cdna_end": null,
"cdna_length": 5067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CLTA",
"gene_hgnc_id": 2090,
"hgvs_c": "n.485+15824T>C",
"hgvs_p": null,
"transcript": "ENST00000464497.5",
"protein_id": "ENSP00000419158.1",
"transcript_support_level": 5,
"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": 1890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"dbsnp": "rs754313408",
"frequency_reference_population": 0.00002912489,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000253155,
"gnomad_genomes_af": 0.0000657099,
"gnomad_exomes_ac": 37,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12012296915054321,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.432,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1026,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.89,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 2,
"pathogenic_score": 3,
"criteria": [
"PM1",
"PP2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005476.7",
"gene_symbol": "GNE",
"hgnc_id": 23657,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1651A>G",
"hgvs_p": "p.Ile551Val"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000464497.5",
"gene_symbol": "CLTA",
"hgnc_id": 2090,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.485+15824T>C",
"hgvs_p": null
}
],
"clinvar_disease": "GNE myopathy,GNE-related disorder,Sialuria,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5 O:1",
"phenotype_combined": "not provided|GNE-related disorder|GNE myopathy|Sialuria;GNE myopathy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}