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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: 2-120989504-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=120989504&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 120989504,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005270.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3539G>T",
"hgvs_p": "p.Gly1180Val",
"transcript": "NM_001374353.1",
"protein_id": "NP_001361282.1",
"transcript_support_level": null,
"aa_start": 1180,
"aa_end": null,
"aa_length": 1569,
"cds_start": 3539,
"cds_end": null,
"cds_length": 4710,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361492.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374353.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3539G>T",
"hgvs_p": "p.Gly1180Val",
"transcript": "ENST00000361492.9",
"protein_id": "ENSP00000354586.5",
"transcript_support_level": 1,
"aa_start": 1180,
"aa_end": null,
"aa_length": 1569,
"cds_start": 3539,
"cds_end": null,
"cds_length": 4710,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001374353.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361492.9"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3590G>T",
"hgvs_p": "p.Gly1197Val",
"transcript": "NM_001371271.1",
"protein_id": "NP_001358200.1",
"transcript_support_level": null,
"aa_start": 1197,
"aa_end": null,
"aa_length": 1586,
"cds_start": 3590,
"cds_end": null,
"cds_length": 4761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371271.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3590G>T",
"hgvs_p": "p.Gly1197Val",
"transcript": "NM_005270.5",
"protein_id": "NP_005261.2",
"transcript_support_level": null,
"aa_start": 1197,
"aa_end": null,
"aa_length": 1586,
"cds_start": 3590,
"cds_end": null,
"cds_length": 4761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005270.5"
},
{
"aa_ref": "G",
"aa_alt": "V",
"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": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3590G>T",
"hgvs_p": "p.Gly1197Val",
"transcript": "ENST00000452319.6",
"protein_id": "ENSP00000390436.1",
"transcript_support_level": 5,
"aa_start": 1197,
"aa_end": null,
"aa_length": 1586,
"cds_start": 3590,
"cds_end": null,
"cds_length": 4761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452319.6"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3533G>T",
"hgvs_p": "p.Gly1178Val",
"transcript": "ENST00000934404.1",
"protein_id": "ENSP00000604463.1",
"transcript_support_level": null,
"aa_start": 1178,
"aa_end": null,
"aa_length": 1567,
"cds_start": 3533,
"cds_end": null,
"cds_length": 4704,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934404.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3476G>T",
"hgvs_p": "p.Gly1159Val",
"transcript": "ENST00000934405.1",
"protein_id": "ENSP00000604464.1",
"transcript_support_level": null,
"aa_start": 1159,
"aa_end": null,
"aa_length": 1548,
"cds_start": 3476,
"cds_end": null,
"cds_length": 4647,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934405.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"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": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3353G>T",
"hgvs_p": "p.Gly1118Val",
"transcript": "ENST00000869361.1",
"protein_id": "ENSP00000539420.1",
"transcript_support_level": null,
"aa_start": 1118,
"aa_end": null,
"aa_length": 1507,
"cds_start": 3353,
"cds_end": null,
"cds_length": 4524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869361.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"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": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3164G>T",
"hgvs_p": "p.Gly1055Val",
"transcript": "NM_001374354.1",
"protein_id": "NP_001361283.1",
"transcript_support_level": null,
"aa_start": 1055,
"aa_end": null,
"aa_length": 1444,
"cds_start": 3164,
"cds_end": null,
"cds_length": 4335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374354.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"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": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3044G>T",
"hgvs_p": "p.Gly1015Val",
"transcript": "ENST00000934406.1",
"protein_id": "ENSP00000604465.1",
"transcript_support_level": null,
"aa_start": 1015,
"aa_end": null,
"aa_length": 1404,
"cds_start": 3044,
"cds_end": null,
"cds_length": 4215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934406.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"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": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3572G>T",
"hgvs_p": "p.Gly1191Val",
"transcript": "XM_011510969.3",
"protein_id": "XP_011509271.3",
"transcript_support_level": null,
"aa_start": 1191,
"aa_end": null,
"aa_length": 1580,
"cds_start": 3572,
"cds_end": null,
"cds_length": 4743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510969.3"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3539G>T",
"hgvs_p": "p.Gly1180Val",
"transcript": "XM_047443947.1",
"protein_id": "XP_047299903.1",
"transcript_support_level": null,
"aa_start": 1180,
"aa_end": null,
"aa_length": 1569,
"cds_start": 3539,
"cds_end": null,
"cds_length": 4710,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443947.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"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": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3521G>T",
"hgvs_p": "p.Gly1174Val",
"transcript": "XM_017003818.2",
"protein_id": "XP_016859307.2",
"transcript_support_level": null,
"aa_start": 1174,
"aa_end": null,
"aa_length": 1563,
"cds_start": 3521,
"cds_end": null,
"cds_length": 4692,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003818.2"
},
{
"aa_ref": "G",
"aa_alt": "V",
"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": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "c.3395G>T",
"hgvs_p": "p.Gly1132Val",
"transcript": "XM_011510971.3",
"protein_id": "XP_011509273.1",
"transcript_support_level": null,
"aa_start": 1132,
"aa_end": null,
"aa_length": 1521,
"cds_start": 3395,
"cds_end": null,
"cds_length": 4566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510971.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "n.*2638G>T",
"hgvs_p": null,
"transcript": "ENST00000341310.10",
"protein_id": "ENSP00000344473.6",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000341310.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "n.*2689G>T",
"hgvs_p": null,
"transcript": "ENST00000445186.5",
"protein_id": "ENSP00000397488.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000445186.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "n.*2638G>T",
"hgvs_p": null,
"transcript": "ENST00000341310.10",
"protein_id": "ENSP00000344473.6",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000341310.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "n.*2689G>T",
"hgvs_p": null,
"transcript": "ENST00000445186.5",
"protein_id": "ENSP00000397488.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000445186.5"
},
{
"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": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "n.*2543+146G>T",
"hgvs_p": null,
"transcript": "ENST00000438299.5",
"protein_id": "ENSP00000400593.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000438299.5"
},
{
"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": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"hgvs_c": "n.*2492+146G>T",
"hgvs_p": null,
"transcript": "ENST00000452692.5",
"protein_id": "ENSP00000403715.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000452692.5"
}
],
"gene_symbol": "GLI2",
"gene_hgnc_id": 4318,
"dbsnp": "rs114823319",
"frequency_reference_population": 0.000019180316,
"hom_count_reference_population": 0,
"allele_count_reference_population": 28,
"gnomad_exomes_af": 0.0000191803,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 28,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.053927212953567505,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.015,
"revel_prediction": "Benign",
"alphamissense_score": 0.0673,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.274,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_005270.5",
"gene_symbol": "GLI2",
"hgnc_id": 4318,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3590G>T",
"hgvs_p": "p.Gly1197Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}