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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: 2-208248388-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=208248388&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 208248388,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000345146.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "NM_005896.4",
"protein_id": "NP_005887.2",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 414,
"cds_start": 395,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 2318,
"mane_select": "ENST00000345146.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"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": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "ENST00000345146.7",
"protein_id": "ENSP00000260985.2",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 414,
"cds_start": 395,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 2318,
"mane_select": "NM_005896.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "ENST00000415913.5",
"protein_id": "ENSP00000390265.1",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 414,
"cds_start": 395,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 777,
"cdna_end": null,
"cdna_length": 2441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "ENST00000446179.5",
"protein_id": "ENSP00000410513.1",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 414,
"cds_start": 395,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 601,
"cdna_end": null,
"cdna_length": 2298,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "NM_001282386.1",
"protein_id": "NP_001269315.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 414,
"cds_start": 395,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 601,
"cdna_end": null,
"cdna_length": 2303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "NM_001282387.1",
"protein_id": "NP_001269316.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 414,
"cds_start": 395,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 758,
"cdna_end": null,
"cdna_length": 2460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His",
"transcript": "ENST00000415282.5",
"protein_id": "ENSP00000391075.1",
"transcript_support_level": 2,
"aa_start": 132,
"aa_end": null,
"aa_length": 156,
"cds_start": 395,
"cds_end": null,
"cds_length": 472,
"cdna_start": 865,
"cdna_end": null,
"cdna_length": 942,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "n.608G>A",
"hgvs_p": null,
"transcript": "ENST00000462386.5",
"protein_id": null,
"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": 1614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.*174G>A",
"hgvs_p": null,
"transcript": "ENST00000417583.5",
"protein_id": "ENSP00000409045.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 72,
"cds_start": -4,
"cds_end": null,
"cds_length": 221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDH1",
"gene_hgnc_id": 5382,
"hgvs_c": "c.*209G>A",
"hgvs_p": null,
"transcript": "ENST00000451391.5",
"protein_id": "ENSP00000396787.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": -4,
"cds_end": null,
"cds_length": 186,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IDH1",
"gene_hgnc_id": 5382,
"dbsnp": "rs121913500",
"frequency_reference_population": 0.000009916146,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000957773,
"gnomad_genomes_af": 0.0000131747,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9793788194656372,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.852,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.992,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.171,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000345146.7",
"gene_symbol": "IDH1",
"hgnc_id": 5382,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.395G>A",
"hgvs_p": "p.Arg132His"
}
],
"clinvar_disease": " somatic,Enchondromatosis,Glioblastoma multiforme,Glioma susceptibility 1,Metaphyseal chondromatosis,Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria,Neoplasm,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:1 US:1",
"phenotype_combined": "Glioblastoma multiforme, somatic|Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria|not provided|Enchondromatosis|Glioma susceptibility 1|Metaphyseal chondromatosis|Neoplasm",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}