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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: 15-90084321-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=90084321&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "IDH2",
"hgnc_id": 5383,
"hgvs_c": "c.1304C>T",
"hgvs_p": "p.Thr435Met",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_002168.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 10124,
"alphamissense_prediction": null,
"alphamissense_score": 0.0956,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.29,
"chr": "15",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "D-2-hydroxyglutaric aciduria 2,Enchondromatosis,IDH2-related disorder,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.009162425994873047,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 452,
"aa_ref": "T",
"aa_start": 435,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2658,
"cdna_start": 1382,
"cds_end": null,
"cds_length": 1359,
"cds_start": 1304,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_002168.4",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1304C>T",
"hgvs_p": "p.Thr435Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000330062.8",
"protein_coding": true,
"protein_id": "NP_002159.2",
"strand": false,
"transcript": "NM_002168.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 452,
"aa_ref": "T",
"aa_start": 435,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2658,
"cdna_start": 1382,
"cds_end": null,
"cds_length": 1359,
"cds_start": 1304,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000330062.8",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1304C>T",
"hgvs_p": "p.Thr435Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002168.4",
"protein_coding": true,
"protein_id": "ENSP00000331897.4",
"strand": false,
"transcript": "ENST00000330062.8",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 480,
"aa_ref": "T",
"aa_start": 463,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2736,
"cdna_start": 1488,
"cds_end": null,
"cds_length": 1443,
"cds_start": 1388,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000864224.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1388C>T",
"hgvs_p": "p.Thr463Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534283.1",
"strand": false,
"transcript": "ENST00000864224.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 475,
"aa_ref": "T",
"aa_start": 458,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1794,
"cdna_start": 1451,
"cds_end": null,
"cds_length": 1428,
"cds_start": 1373,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000864227.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1373C>T",
"hgvs_p": "p.Thr458Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534286.1",
"strand": false,
"transcript": "ENST00000864227.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 451,
"aa_ref": "T",
"aa_start": 434,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1718,
"cdna_start": 1379,
"cds_end": null,
"cds_length": 1356,
"cds_start": 1301,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000864229.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1301C>T",
"hgvs_p": "p.Thr434Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534288.1",
"strand": false,
"transcript": "ENST00000864229.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 450,
"aa_ref": "T",
"aa_start": 433,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2646,
"cdna_start": 1376,
"cds_end": null,
"cds_length": 1353,
"cds_start": 1298,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000864223.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1298C>T",
"hgvs_p": "p.Thr433Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534282.1",
"strand": false,
"transcript": "ENST00000864223.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 443,
"aa_ref": "T",
"aa_start": 426,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1698,
"cdna_start": 1355,
"cds_end": null,
"cds_length": 1332,
"cds_start": 1277,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000864228.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1277C>T",
"hgvs_p": "p.Thr426Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534287.1",
"strand": false,
"transcript": "ENST00000864228.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 441,
"aa_ref": "T",
"aa_start": 424,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2598,
"cdna_start": 1350,
"cds_end": null,
"cds_length": 1326,
"cds_start": 1271,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000864225.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1271C>T",
"hgvs_p": "p.Thr424Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534284.1",
"strand": false,
"transcript": "ENST00000864225.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 421,
"aa_ref": "T",
"aa_start": 404,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2573,
"cdna_start": 1301,
"cds_end": null,
"cds_length": 1266,
"cds_start": 1211,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000864221.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1211C>T",
"hgvs_p": "p.Thr404Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534280.1",
"strand": false,
"transcript": "ENST00000864221.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 415,
"aa_ref": "T",
"aa_start": 398,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1619,
"cdna_start": 1282,
"cds_end": null,
"cds_length": 1248,
"cds_start": 1193,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000948834.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1193C>T",
"hgvs_p": "p.Thr398Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618893.1",
"strand": false,
"transcript": "ENST00000948834.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 413,
"aa_ref": "T",
"aa_start": 396,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1603,
"cdna_start": 1264,
"cds_end": null,
"cds_length": 1242,
"cds_start": 1187,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000948835.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1187C>T",
"hgvs_p": "p.Thr396Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618894.1",
"strand": false,
"transcript": "ENST00000948835.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 408,
"aa_ref": "T",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2447,
"cdna_start": 1239,
"cds_end": null,
"cds_length": 1227,
"cds_start": 1172,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000864226.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1172C>T",
"hgvs_p": "p.Thr391Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534285.1",
"strand": false,
"transcript": "ENST00000864226.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 404,
"aa_ref": "T",
"aa_start": 387,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2520,
"cdna_start": 1244,
"cds_end": null,
"cds_length": 1215,
"cds_start": 1160,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000864222.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1160C>T",
"hgvs_p": "p.Thr387Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534281.1",
"strand": false,
"transcript": "ENST00000864222.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 400,
"aa_ref": "T",
"aa_start": 383,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1578,
"cdna_start": 1235,
"cds_end": null,
"cds_length": 1203,
"cds_start": 1148,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001289910.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1148C>T",
"hgvs_p": "p.Thr383Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001276839.1",
"strand": false,
"transcript": "NM_001289910.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 400,
"aa_ref": "T",
"aa_start": 383,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1453,
"cdna_start": 1309,
"cds_end": null,
"cds_length": 1203,
"cds_start": 1148,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000540499.2",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.1148C>T",
"hgvs_p": "p.Thr383Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000446147.2",
"strand": false,
"transcript": "ENST00000540499.2",
"transcript_support_level": 2
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 322,
"aa_ref": "T",
"aa_start": 305,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2400,
"cdna_start": 1124,
"cds_end": null,
"cds_length": 969,
"cds_start": 914,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001290114.2",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.914C>T",
"hgvs_p": "p.Thr305Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001277043.1",
"strand": false,
"transcript": "NM_001290114.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 312,
"aa_ref": "T",
"aa_start": 295,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1278,
"cdna_start": 971,
"cds_end": null,
"cds_length": 939,
"cds_start": 884,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000559482.5",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "c.884C>T",
"hgvs_p": "p.Thr295Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000453016.1",
"strand": false,
"transcript": "ENST00000559482.5",
"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": 1449,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000560061.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "n.*929C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453254.1",
"strand": false,
"transcript": "ENST00000560061.1",
"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": 1449,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000560061.1",
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"hgvs_c": "n.*929C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453254.1",
"strand": false,
"transcript": "ENST00000560061.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs118053940",
"effect": "missense_variant",
"frequency_reference_population": 0.0062724515,
"gene_hgnc_id": 5383,
"gene_symbol": "IDH2",
"gnomad_exomes_ac": 9579,
"gnomad_exomes_af": 0.00655304,
"gnomad_exomes_homalt": 52,
"gnomad_genomes_ac": 545,
"gnomad_genomes_af": 0.00357898,
"gnomad_genomes_homalt": 3,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 55,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|not provided|D-2-hydroxyglutaric aciduria 2|IDH2-related disorder|Enchondromatosis",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.114,
"pos": 90084321,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.103,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002168.4"
}
]
}