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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: 15-90085305-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=90085305&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 90085305,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000330062.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.1050C>T",
"hgvs_p": "p.Thr350Thr",
"transcript": "NM_002168.4",
"protein_id": "NP_002159.2",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 452,
"cds_start": 1050,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 1128,
"cdna_end": null,
"cdna_length": 2658,
"mane_select": "ENST00000330062.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.1050C>T",
"hgvs_p": "p.Thr350Thr",
"transcript": "ENST00000330062.8",
"protein_id": "ENSP00000331897.4",
"transcript_support_level": 1,
"aa_start": 350,
"aa_end": null,
"aa_length": 452,
"cds_start": 1050,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 1128,
"cdna_end": null,
"cdna_length": 2658,
"mane_select": "NM_002168.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.894C>T",
"hgvs_p": "p.Thr298Thr",
"transcript": "NM_001289910.1",
"protein_id": "NP_001276839.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 400,
"cds_start": 894,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 981,
"cdna_end": null,
"cdna_length": 1578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.894C>T",
"hgvs_p": "p.Thr298Thr",
"transcript": "ENST00000540499.2",
"protein_id": "ENSP00000446147.2",
"transcript_support_level": 2,
"aa_start": 298,
"aa_end": null,
"aa_length": 400,
"cds_start": 894,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 1055,
"cdna_end": null,
"cdna_length": 1453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.660C>T",
"hgvs_p": "p.Thr220Thr",
"transcript": "NM_001290114.2",
"protein_id": "NP_001277043.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 322,
"cds_start": 660,
"cds_end": null,
"cds_length": 969,
"cdna_start": 870,
"cdna_end": null,
"cdna_length": 2400,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "c.723C>T",
"hgvs_p": "p.Thr241Thr",
"transcript": "ENST00000559482.5",
"protein_id": "ENSP00000453016.1",
"transcript_support_level": 5,
"aa_start": 241,
"aa_end": null,
"aa_length": 312,
"cds_start": 723,
"cds_end": null,
"cds_length": 939,
"cdna_start": 810,
"cdna_end": null,
"cdna_length": 1278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "n.*675C>T",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"hgvs_c": "n.*675C>T",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IDH2",
"gene_hgnc_id": 5383,
"dbsnp": "rs11540478",
"frequency_reference_population": 0.015558082,
"hom_count_reference_population": 1600,
"allele_count_reference_population": 24143,
"gnomad_exomes_af": 0.0116125,
"gnomad_genomes_af": 0.0518692,
"gnomad_exomes_ac": 16254,
"gnomad_genomes_ac": 7889,
"gnomad_exomes_homalt": 1080,
"gnomad_genomes_homalt": 520,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8799999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.88,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -5.168,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000330062.8",
"gene_symbol": "IDH2",
"hgnc_id": 5383,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1050C>T",
"hgvs_p": "p.Thr350Thr"
}
],
"clinvar_disease": "D-2-hydroxyglutaric aciduria 2,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "not specified|D-2-hydroxyglutaric aciduria 2|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}