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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: 2-120989857-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=120989857&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GLI2",
"hgnc_id": 4318,
"hgvs_c": "c.3943C>T",
"hgvs_p": "p.Pro1315Ser",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_005270.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 38992,
"alphamissense_prediction": null,
"alphamissense_score": 0.0613,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.79,
"chr": "2",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Holoprosencephaly 9,Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:5",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.003306269645690918,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1569,
"aa_ref": "P",
"aa_start": 1298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7136,
"cdna_start": 4340,
"cds_end": null,
"cds_length": 4710,
"cds_start": 3892,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_001374353.1",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3892C>T",
"hgvs_p": "p.Pro1298Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000361492.9",
"protein_coding": true,
"protein_id": "NP_001361282.1",
"strand": true,
"transcript": "NM_001374353.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1569,
"aa_ref": "P",
"aa_start": 1298,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7136,
"cdna_start": 4340,
"cds_end": null,
"cds_length": 4710,
"cds_start": 3892,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000361492.9",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3892C>T",
"hgvs_p": "p.Pro1298Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001374353.1",
"protein_coding": true,
"protein_id": "ENSP00000354586.5",
"strand": true,
"transcript": "ENST00000361492.9",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1586,
"aa_ref": "P",
"aa_start": 1315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7187,
"cdna_start": 4391,
"cds_end": null,
"cds_length": 4761,
"cds_start": 3943,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_001371271.1",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3943C>T",
"hgvs_p": "p.Pro1315Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001358200.1",
"strand": true,
"transcript": "NM_001371271.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1586,
"aa_ref": "P",
"aa_start": 1315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6927,
"cdna_start": 4131,
"cds_end": null,
"cds_length": 4761,
"cds_start": 3943,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_005270.5",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3943C>T",
"hgvs_p": "p.Pro1315Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_005261.2",
"strand": true,
"transcript": "NM_005270.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1586,
"aa_ref": "P",
"aa_start": 1315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4761,
"cdna_start": 3943,
"cds_end": null,
"cds_length": 4761,
"cds_start": 3943,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000452319.6",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3943C>T",
"hgvs_p": "p.Pro1315Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000390436.1",
"strand": true,
"transcript": "ENST00000452319.6",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1567,
"aa_ref": "P",
"aa_start": 1296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6981,
"cdna_start": 4339,
"cds_end": null,
"cds_length": 4704,
"cds_start": 3886,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000934404.1",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3886C>T",
"hgvs_p": "p.Pro1296Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604463.1",
"strand": true,
"transcript": "ENST00000934404.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1548,
"aa_ref": "P",
"aa_start": 1277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6919,
"cdna_start": 4277,
"cds_end": null,
"cds_length": 4647,
"cds_start": 3829,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000934405.1",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3829C>T",
"hgvs_p": "p.Pro1277Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604464.1",
"strand": true,
"transcript": "ENST00000934405.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1507,
"aa_ref": "P",
"aa_start": 1236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6818,
"cdna_start": 4176,
"cds_end": null,
"cds_length": 4524,
"cds_start": 3706,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000869361.1",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3706C>T",
"hgvs_p": "p.Pro1236Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539420.1",
"strand": true,
"transcript": "ENST00000869361.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1444,
"aa_ref": "P",
"aa_start": 1173,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7030,
"cdna_start": 4234,
"cds_end": null,
"cds_length": 4335,
"cds_start": 3517,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001374354.1",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3517C>T",
"hgvs_p": "p.Pro1173Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001361283.1",
"strand": true,
"transcript": "NM_001374354.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1404,
"aa_ref": "P",
"aa_start": 1133,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6248,
"cdna_start": 3609,
"cds_end": null,
"cds_length": 4215,
"cds_start": 3397,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000934406.1",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3397C>T",
"hgvs_p": "p.Pro1133Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604465.1",
"strand": true,
"transcript": "ENST00000934406.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1580,
"aa_ref": "P",
"aa_start": 1309,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6730,
"cdna_start": 3934,
"cds_end": null,
"cds_length": 4743,
"cds_start": 3925,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_011510969.3",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3925C>T",
"hgvs_p": "p.Pro1309Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011509271.3",
"strand": true,
"transcript": "XM_011510969.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1569,
"aa_ref": "P",
"aa_start": 1298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6876,
"cdna_start": 4080,
"cds_end": null,
"cds_length": 4710,
"cds_start": 3892,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_047443947.1",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3892C>T",
"hgvs_p": "p.Pro1298Ser",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299903.1",
"strand": true,
"transcript": "XM_047443947.1",
"transcript_support_level": null
},
{
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"aa_ref": "P",
"aa_start": 1292,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6679,
"cdna_start": 3883,
"cds_end": null,
"cds_length": 4692,
"cds_start": 3874,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_017003818.2",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3874C>T",
"hgvs_p": "p.Pro1292Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016859307.2",
"strand": true,
"transcript": "XM_017003818.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1521,
"aa_ref": "P",
"aa_start": 1250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6705,
"cdna_start": 3909,
"cds_end": null,
"cds_length": 4566,
"cds_start": 3748,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_011510971.3",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "c.3748C>T",
"hgvs_p": "p.Pro1250Ser",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011509273.1",
"strand": true,
"transcript": "XM_011510971.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4904,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000341310.10",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "n.*2991C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000344473.6",
"strand": true,
"transcript": "ENST00000341310.10",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4955,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000445186.5",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "n.*3042C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000397488.1",
"strand": true,
"transcript": "ENST00000445186.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
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"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4904,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000341310.10",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "n.*2991C>T",
"hgvs_p": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000344473.6",
"strand": true,
"transcript": "ENST00000341310.10",
"transcript_support_level": 2
},
{
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"biotype": "nonsense_mediated_decay",
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"cdna_end": null,
"cdna_length": 4955,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000445186.5",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "n.*3042C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000397488.1",
"strand": true,
"transcript": "ENST00000445186.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
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"aa_ref": null,
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"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3724,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000438299.5",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "n.*2543+499C>T",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000400593.1",
"strand": true,
"transcript": "ENST00000438299.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3673,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000452692.5",
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"hgvs_c": "n.*2492+499C>T",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000403715.1",
"strand": true,
"transcript": "ENST00000452692.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs114376238",
"effect": "missense_variant",
"frequency_reference_population": 0.024174038,
"gene_hgnc_id": 4318,
"gene_symbol": "GLI2",
"gnomad_exomes_ac": 36430,
"gnomad_exomes_af": 0.0249416,
"gnomad_exomes_homalt": 553,
"gnomad_genomes_ac": 2562,
"gnomad_genomes_af": 0.0168157,
"gnomad_genomes_homalt": 35,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 588,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|not provided|Holoprosencephaly 9|Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome;Holoprosencephaly 9",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.031,
"pos": 120989857,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.017,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005270.5"
}
]
}