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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: 5-97163077-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=97163077&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RIOK2",
"hgnc_id": 18999,
"hgvs_c": "c.1643G>C",
"hgvs_p": "p.Ser548Thr",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_018343.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LIX1-AS1",
"hgnc_id": 52976,
"hgvs_c": "n.574-19931C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000504578.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 2,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0802,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.42,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.11932194232940674,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 552,
"aa_ref": "S",
"aa_start": 548,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3909,
"cdna_start": 1699,
"cds_end": null,
"cds_length": 1659,
"cds_start": 1643,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_018343.3",
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"hgvs_c": "c.1643G>C",
"hgvs_p": "p.Ser548Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000283109.8",
"protein_coding": true,
"protein_id": "NP_060813.2",
"strand": false,
"transcript": "NM_018343.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 552,
"aa_ref": "S",
"aa_start": 548,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3909,
"cdna_start": 1699,
"cds_end": null,
"cds_length": 1659,
"cds_start": 1643,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000283109.8",
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"hgvs_c": "c.1643G>C",
"hgvs_p": "p.Ser548Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018343.3",
"protein_coding": true,
"protein_id": "ENSP00000283109.3",
"strand": false,
"transcript": "ENST00000283109.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 551,
"aa_ref": "S",
"aa_start": 547,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3936,
"cdna_start": 1730,
"cds_end": null,
"cds_length": 1656,
"cds_start": 1640,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000924329.1",
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"hgvs_c": "c.1640G>C",
"hgvs_p": "p.Ser547Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594388.1",
"strand": false,
"transcript": "ENST00000924329.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 551,
"aa_ref": "S",
"aa_start": 547,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3612,
"cdna_start": 1738,
"cds_end": null,
"cds_length": 1656,
"cds_start": 1640,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000924331.1",
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"hgvs_c": "c.1640G>C",
"hgvs_p": "p.Ser547Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594390.1",
"strand": false,
"transcript": "ENST00000924331.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 548,
"aa_ref": "S",
"aa_start": 544,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3893,
"cdna_start": 1685,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1631,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000924330.1",
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"hgvs_c": "c.1631G>C",
"hgvs_p": "p.Ser544Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594389.1",
"strand": false,
"transcript": "ENST00000924330.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 521,
"aa_ref": "S",
"aa_start": 517,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1713,
"cdna_start": 1570,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1550,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000902084.1",
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"hgvs_c": "c.1550G>C",
"hgvs_p": "p.Ser517Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572143.1",
"strand": false,
"transcript": "ENST00000902084.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 158,
"aa_ref": "S",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 603,
"cdna_start": 462,
"cds_end": null,
"cds_length": 477,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000511293.1",
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"hgvs_c": "c.461G>C",
"hgvs_p": "p.Ser154Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000421830.1",
"strand": false,
"transcript": "ENST00000511293.1",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 365,
"aa_ref": "S",
"aa_start": 361,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3532,
"cdna_start": 1322,
"cds_end": null,
"cds_length": 1098,
"cds_start": 1082,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_017009628.2",
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"hgvs_c": "c.1082G>C",
"hgvs_p": "p.Ser361Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016865117.1",
"strand": false,
"transcript": "XM_017009628.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1793,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000504578.2",
"gene_hgnc_id": 52976,
"gene_symbol": "LIX1-AS1",
"hgvs_c": "n.574-19931C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000504578.2",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs147011890",
"effect": "missense_variant",
"frequency_reference_population": 0.0000013699981,
"gene_hgnc_id": 18999,
"gene_symbol": "RIOK2",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000137,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.873,
"pos": 97163077,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.099,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_018343.3"
}
]
}