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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: 9-36222885-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=36222885&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 36222885,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005476.7",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1618C>T",
"hgvs_p": "p.His540Tyr",
"transcript": "NM_001128227.3",
"protein_id": "NP_001121699.1",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 753,
"cds_start": 1618,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 5220,
"mane_select": null,
"mane_plus": "ENST00000396594.8",
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1618C>T",
"hgvs_p": "p.His540Tyr",
"transcript": "ENST00000396594.8",
"protein_id": "ENSP00000379839.3",
"transcript_support_level": 1,
"aa_start": 540,
"aa_end": null,
"aa_length": 753,
"cds_start": 1618,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 5220,
"mane_select": null,
"mane_plus": "NM_001128227.3",
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1525C>T",
"hgvs_p": "p.His509Tyr",
"transcript": "NM_005476.7",
"protein_id": "NP_005467.1",
"transcript_support_level": null,
"aa_start": 509,
"aa_end": null,
"aa_length": 722,
"cds_start": 1525,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 1695,
"cdna_end": null,
"cdna_length": 5263,
"mane_select": "ENST00000642385.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1525C>T",
"hgvs_p": "p.His509Tyr",
"transcript": "ENST00000642385.2",
"protein_id": "ENSP00000494141.2",
"transcript_support_level": null,
"aa_start": 509,
"aa_end": null,
"aa_length": 722,
"cds_start": 1525,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 1695,
"cdna_end": null,
"cdna_length": 5263,
"mane_select": "NM_005476.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.His450Tyr",
"transcript": "ENST00000543356.7",
"protein_id": "ENSP00000437765.3",
"transcript_support_level": 1,
"aa_start": 450,
"aa_end": null,
"aa_length": 663,
"cds_start": 1348,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 1510,
"cdna_end": null,
"cdna_length": 2576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1372C>T",
"hgvs_p": "p.His458Tyr",
"transcript": "NM_001374797.1",
"protein_id": "NP_001361726.1",
"transcript_support_level": null,
"aa_start": 458,
"aa_end": null,
"aa_length": 671,
"cds_start": 1372,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1542,
"cdna_end": null,
"cdna_length": 5110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.His450Tyr",
"transcript": "NM_001190388.2",
"protein_id": "NP_001177317.2",
"transcript_support_level": null,
"aa_start": 450,
"aa_end": null,
"aa_length": 663,
"cds_start": 1348,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 1446,
"cdna_end": null,
"cdna_length": 5014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.His450Tyr",
"transcript": "NM_001374798.1",
"protein_id": "NP_001361727.1",
"transcript_support_level": null,
"aa_start": 450,
"aa_end": null,
"aa_length": 663,
"cds_start": 1348,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 1489,
"cdna_end": null,
"cdna_length": 5057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1195C>T",
"hgvs_p": "p.His399Tyr",
"transcript": "NM_001190384.3",
"protein_id": "NP_001177313.1",
"transcript_support_level": null,
"aa_start": 399,
"aa_end": null,
"aa_length": 612,
"cds_start": 1195,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1336,
"cdna_end": null,
"cdna_length": 4904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1195C>T",
"hgvs_p": "p.His399Tyr",
"transcript": "ENST00000539208.5",
"protein_id": "ENSP00000445117.1",
"transcript_support_level": 2,
"aa_start": 399,
"aa_end": null,
"aa_length": 612,
"cds_start": 1195,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1333,
"cdna_end": null,
"cdna_length": 2190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1525C>T",
"hgvs_p": "p.His509Tyr",
"transcript": "XM_017014167.1",
"protein_id": "XP_016869656.1",
"transcript_support_level": null,
"aa_start": 509,
"aa_end": null,
"aa_length": 722,
"cds_start": 1525,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 1591,
"cdna_end": null,
"cdna_length": 5159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1465C>T",
"hgvs_p": "p.His489Tyr",
"transcript": "XM_005251334.5",
"protein_id": "XP_005251391.1",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 702,
"cds_start": 1465,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1499,
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1411+488C>T",
"hgvs_p": null,
"transcript": "NM_001190383.3",
"protein_id": "NP_001177312.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 648,
"cds_start": -4,
"cds_end": null,
"cds_length": 1947,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "GNE",
"gene_hgnc_id": 23657,
"hgvs_c": "c.1411+488C>T",
"hgvs_p": null,
"transcript": "ENST00000447283.6",
"protein_id": "ENSP00000414760.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 648,
"cds_start": -4,
"cds_end": null,
"cds_length": 1947,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2174,
"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+18706G>A",
"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": "rs754892377",
"frequency_reference_population": 0.0000027363337,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273633,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5693570375442505,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.20000000298023224,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.575,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2101,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.384,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.2,
"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": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_005476.7",
"gene_symbol": "GNE",
"hgnc_id": 23657,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1525C>T",
"hgvs_p": "p.His509Tyr"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000464497.5",
"gene_symbol": "CLTA",
"hgnc_id": 2090,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.485+18706G>A",
"hgvs_p": null
}
],
"clinvar_disease": "GNE myopathy,Sialuria",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "GNE myopathy|Sialuria;GNE myopathy",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}