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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: 2-210592937-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=210592937&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 210592937,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000233072.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1145C>T",
"hgvs_p": "p.Pro382Leu",
"transcript": "NM_001875.5",
"protein_id": "NP_001866.2",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 1500,
"cds_start": 1145,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 1280,
"cdna_end": null,
"cdna_length": 5760,
"mane_select": "ENST00000233072.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1145C>T",
"hgvs_p": "p.Pro382Leu",
"transcript": "ENST00000233072.10",
"protein_id": "ENSP00000233072.5",
"transcript_support_level": 1,
"aa_start": 382,
"aa_end": null,
"aa_length": 1500,
"cds_start": 1145,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 1280,
"cdna_end": null,
"cdna_length": 5760,
"mane_select": "NM_001875.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1163C>T",
"hgvs_p": "p.Pro388Leu",
"transcript": "ENST00000430249.7",
"protein_id": "ENSP00000402608.2",
"transcript_support_level": 1,
"aa_start": 388,
"aa_end": null,
"aa_length": 1506,
"cds_start": 1163,
"cds_end": null,
"cds_length": 4521,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 5723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1178C>T",
"hgvs_p": "p.Pro393Leu",
"transcript": "NM_001369256.1",
"protein_id": "NP_001356185.1",
"transcript_support_level": null,
"aa_start": 393,
"aa_end": null,
"aa_length": 1511,
"cds_start": 1178,
"cds_end": null,
"cds_length": 4536,
"cdna_start": 1227,
"cdna_end": null,
"cdna_length": 5707,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1145C>T",
"hgvs_p": "p.Pro382Leu",
"transcript": "NM_001122633.3",
"protein_id": "NP_001116105.2",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 1500,
"cds_start": 1145,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 1242,
"cdna_end": null,
"cdna_length": 5722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1145C>T",
"hgvs_p": "p.Pro382Leu",
"transcript": "NM_001369257.1",
"protein_id": "NP_001356186.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 1500,
"cds_start": 1145,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 1362,
"cdna_end": null,
"cdna_length": 5842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1145C>T",
"hgvs_p": "p.Pro382Leu",
"transcript": "ENST00000673510.1",
"protein_id": "ENSP00000500537.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 1500,
"cds_start": 1145,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 1365,
"cdna_end": null,
"cdna_length": 4880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1145C>T",
"hgvs_p": "p.Pro382Leu",
"transcript": "ENST00000673630.1",
"protein_id": "ENSP00000501073.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 1500,
"cds_start": 1145,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 1479,
"cdna_end": null,
"cdna_length": 5775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1145C>T",
"hgvs_p": "p.Pro382Leu",
"transcript": "ENST00000673711.1",
"protein_id": "ENSP00000501022.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 1500,
"cds_start": 1145,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 1218,
"cdna_end": null,
"cdna_length": 5698,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "n.2057C>T",
"hgvs_p": null,
"transcript": "NR_161225.1",
"protein_id": null,
"transcript_support_level": null,
"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": 6534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"dbsnp": "rs201407486",
"frequency_reference_population": 0.00002670578,
"hom_count_reference_population": 0,
"allele_count_reference_population": 39,
"gnomad_exomes_af": 0.0000267058,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 39,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6566545367240906,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.692,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.275,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.921,
"phylop100way_prediction": "Uncertain_significance",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000233072.10",
"gene_symbol": "CPS1",
"hgnc_id": 2323,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1145C>T",
"hgvs_p": "p.Pro382Leu"
}
],
"clinvar_disease": " neonatal, susceptibility to, type I,Congenital hyperammonemia,Pulmonary hypertension",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:4",
"phenotype_combined": "Congenital hyperammonemia, type I|Pulmonary hypertension, neonatal, susceptibility to|Pulmonary hypertension, neonatal, susceptibility to;Congenital hyperammonemia, type I",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}