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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: 3-122740607-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=122740607&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "HSPBAP1",
"hgnc_id": 16389,
"hgvs_c": "c.1205C>T",
"hgvs_p": "p.Pro402Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_024610.6",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 22,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0575,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.71,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0337444543838501,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 488,
"aa_ref": "P",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1964,
"cdna_start": 1356,
"cds_end": null,
"cds_length": 1467,
"cds_start": 1205,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_024610.6",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1205C>T",
"hgvs_p": "p.Pro402Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000306103.3",
"protein_coding": true,
"protein_id": "NP_078886.2",
"strand": false,
"transcript": "NM_024610.6",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 488,
"aa_ref": "P",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1964,
"cdna_start": 1356,
"cds_end": null,
"cds_length": 1467,
"cds_start": 1205,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000306103.3",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1205C>T",
"hgvs_p": "p.Pro402Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024610.6",
"protein_coding": true,
"protein_id": "ENSP00000302562.2",
"strand": false,
"transcript": "ENST00000306103.3",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1647,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000471534.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "n.1043C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000471534.1",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 492,
"aa_ref": "P",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1699,
"cdna_start": 1355,
"cds_end": null,
"cds_length": 1479,
"cds_start": 1217,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000936102.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Pro406Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606161.1",
"strand": false,
"transcript": "ENST00000936102.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 460,
"aa_ref": "P",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1880,
"cdna_start": 1272,
"cds_end": null,
"cds_length": 1383,
"cds_start": 1121,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001320728.2",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1121C>T",
"hgvs_p": "p.Pro374Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001307657.1",
"strand": false,
"transcript": "NM_001320728.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 460,
"aa_ref": "P",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1619,
"cdna_start": 1268,
"cds_end": null,
"cds_length": 1383,
"cds_start": 1121,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000877417.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1121C>T",
"hgvs_p": "p.Pro374Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547476.1",
"strand": false,
"transcript": "ENST00000877417.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 451,
"aa_ref": "P",
"aa_start": 365,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1811,
"cdna_start": 1204,
"cds_end": null,
"cds_length": 1356,
"cds_start": 1094,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000877416.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1094C>T",
"hgvs_p": "p.Pro365Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547475.1",
"strand": false,
"transcript": "ENST00000877416.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 430,
"aa_ref": "P",
"aa_start": 344,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1776,
"cdna_start": 1150,
"cds_end": null,
"cds_length": 1293,
"cds_start": 1031,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000971052.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1031C>T",
"hgvs_p": "p.Pro344Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641111.1",
"strand": false,
"transcript": "ENST00000971052.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 426,
"aa_ref": "P",
"aa_start": 340,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1770,
"cdna_start": 1168,
"cds_end": null,
"cds_length": 1281,
"cds_start": 1019,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000877414.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Pro340Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547473.1",
"strand": false,
"transcript": "ENST00000877414.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 398,
"aa_ref": "P",
"aa_start": 312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1662,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 1197,
"cds_start": 935,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000877415.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.935C>T",
"hgvs_p": "p.Pro312Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547474.1",
"strand": false,
"transcript": "ENST00000877415.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 385,
"aa_ref": "P",
"aa_start": 299,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1518,
"cdna_start": 917,
"cds_end": null,
"cds_length": 1158,
"cds_start": 896,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000936101.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.896C>T",
"hgvs_p": "p.Pro299Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606160.1",
"strand": false,
"transcript": "ENST00000936101.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 357,
"aa_ref": "P",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1528,
"cdna_start": 922,
"cds_end": null,
"cds_length": 1074,
"cds_start": 812,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000936099.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.812C>T",
"hgvs_p": "p.Pro271Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606158.1",
"strand": false,
"transcript": "ENST00000936099.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 295,
"aa_ref": "P",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1265,
"cdna_start": 660,
"cds_end": null,
"cds_length": 888,
"cds_start": 626,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000936100.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.626C>T",
"hgvs_p": "p.Pro209Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606159.1",
"strand": false,
"transcript": "ENST00000936100.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 451,
"aa_ref": "P",
"aa_start": 365,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9042,
"cdna_start": 8434,
"cds_end": null,
"cds_length": 1356,
"cds_start": 1094,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047448918.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1094C>T",
"hgvs_p": "p.Pro365Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304874.1",
"strand": false,
"transcript": "XM_047448918.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 426,
"aa_ref": "P",
"aa_start": 340,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1778,
"cdna_start": 1170,
"cds_end": null,
"cds_length": 1281,
"cds_start": 1019,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_017007179.2",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Pro340Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016862668.1",
"strand": false,
"transcript": "XM_017007179.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 398,
"aa_ref": "P",
"aa_start": 312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1694,
"cdna_start": 1086,
"cds_end": null,
"cds_length": 1197,
"cds_start": 935,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047448919.1",
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"hgvs_c": "c.935C>T",
"hgvs_p": "p.Pro312Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304875.1",
"strand": false,
"transcript": "XM_047448919.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs371225480",
"effect": "missense_variant",
"frequency_reference_population": 0.000013630681,
"gene_hgnc_id": 16389,
"gene_symbol": "HSPBAP1",
"gnomad_exomes_ac": 15,
"gnomad_exomes_af": 0.0000102609,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 7,
"gnomad_genomes_af": 0.0000460072,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.466,
"pos": 122740607,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.025,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024610.6"
}
]
}