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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: 15-90088702-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=90088702&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 90088702,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002168.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "NM_002168.4",
"protein_id": "NP_002159.2",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 452,
"cds_start": 419,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000330062.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002168.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000330062.8",
"protein_id": "ENSP00000331897.4",
"transcript_support_level": 1,
"aa_start": 140,
"aa_end": null,
"aa_length": 452,
"cds_start": 419,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002168.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000330062.8"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.503G>A",
"hgvs_p": "p.Arg168Gln",
"transcript": "ENST00000864224.1",
"protein_id": "ENSP00000534283.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 480,
"cds_start": 503,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864224.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.488G>A",
"hgvs_p": "p.Arg163Gln",
"transcript": "ENST00000864227.1",
"protein_id": "ENSP00000534286.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 475,
"cds_start": 488,
"cds_end": null,
"cds_length": 1428,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864227.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000864229.1",
"protein_id": "ENSP00000534288.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 451,
"cds_start": 419,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864229.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000864223.1",
"protein_id": "ENSP00000534282.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 450,
"cds_start": 419,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864223.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.392G>A",
"hgvs_p": "p.Arg131Gln",
"transcript": "ENST00000864228.1",
"protein_id": "ENSP00000534287.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 443,
"cds_start": 392,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864228.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000864225.1",
"protein_id": "ENSP00000534284.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 441,
"cds_start": 419,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864225.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000864221.1",
"protein_id": "ENSP00000534280.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 421,
"cds_start": 419,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864221.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000948834.1",
"protein_id": "ENSP00000618893.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 415,
"cds_start": 419,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948834.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000948835.1",
"protein_id": "ENSP00000618894.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 413,
"cds_start": 419,
"cds_end": null,
"cds_length": 1242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948835.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.287G>A",
"hgvs_p": "p.Arg96Gln",
"transcript": "ENST00000864226.1",
"protein_id": "ENSP00000534285.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 408,
"cds_start": 287,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864226.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000864222.1",
"protein_id": "ENSP00000534281.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 404,
"cds_start": 419,
"cds_end": null,
"cds_length": 1215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864222.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.263G>A",
"hgvs_p": "p.Arg88Gln",
"transcript": "NM_001289910.1",
"protein_id": "NP_001276839.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 400,
"cds_start": 263,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001289910.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.263G>A",
"hgvs_p": "p.Arg88Gln",
"transcript": "ENST00000540499.2",
"protein_id": "ENSP00000446147.2",
"transcript_support_level": 2,
"aa_start": 88,
"aa_end": null,
"aa_length": 400,
"cds_start": 263,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540499.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.29G>A",
"hgvs_p": "p.Arg10Gln",
"transcript": "NM_001290114.2",
"protein_id": "NP_001277043.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 322,
"cds_start": 29,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290114.2"
},
{
"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": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.208-200G>A",
"hgvs_p": null,
"transcript": "ENST00000559482.5",
"protein_id": "ENSP00000453016.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 312,
"cds_start": null,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000559482.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "n.*44G>A",
"hgvs_p": null,
"transcript": "ENST00000560061.1",
"protein_id": "ENSP00000453254.1",
"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": "ENST00000560061.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "n.*44G>A",
"hgvs_p": null,
"transcript": "ENST00000560061.1",
"protein_id": "ENSP00000453254.1",
"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": "ENST00000560061.1"
}
],
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"dbsnp": "rs121913502",
"frequency_reference_population": 0.000043996846,
"hom_count_reference_population": 0,
"allele_count_reference_population": 71,
"gnomad_exomes_af": 0.0000417314,
"gnomad_genomes_af": 0.00006578,
"gnomad_exomes_ac": 61,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9197206497192383,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.891,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9872,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM5,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM5",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_002168.4",
"gene_symbol": "IDH2",
"hgnc_id": 5383,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln"
}
],
"clinvar_disease": "D-2-hydroxyglutaric aciduria 2,Inborn genetic diseases,Neoplasm,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1 US:1",
"phenotype_combined": "D-2-hydroxyglutaric aciduria 2|not provided|Inborn genetic diseases|Neoplasm",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}