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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: 2-210642571-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=210642571&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 210642571,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000233072.10",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3047A>G",
"hgvs_p": "p.Asn1016Ser",
"transcript": "NM_001875.5",
"protein_id": "NP_001866.2",
"transcript_support_level": null,
"aa_start": 1016,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3047,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 3182,
"cdna_end": null,
"cdna_length": 5760,
"mane_select": "ENST00000233072.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3047A>G",
"hgvs_p": "p.Asn1016Ser",
"transcript": "ENST00000233072.10",
"protein_id": "ENSP00000233072.5",
"transcript_support_level": 1,
"aa_start": 1016,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3047,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 3182,
"cdna_end": null,
"cdna_length": 5760,
"mane_select": "NM_001875.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3065A>G",
"hgvs_p": "p.Asn1022Ser",
"transcript": "ENST00000430249.7",
"protein_id": "ENSP00000402608.2",
"transcript_support_level": 1,
"aa_start": 1022,
"aa_end": null,
"aa_length": 1506,
"cds_start": 3065,
"cds_end": null,
"cds_length": 4521,
"cdna_start": 3147,
"cdna_end": null,
"cdna_length": 5723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.1694A>G",
"hgvs_p": "p.Asn565Ser",
"transcript": "ENST00000451903.3",
"protein_id": "ENSP00000406136.2",
"transcript_support_level": 1,
"aa_start": 565,
"aa_end": null,
"aa_length": 1049,
"cds_start": 1694,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 2203,
"cdna_end": null,
"cdna_length": 4779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3080A>G",
"hgvs_p": "p.Asn1027Ser",
"transcript": "NM_001369256.1",
"protein_id": "NP_001356185.1",
"transcript_support_level": null,
"aa_start": 1027,
"aa_end": null,
"aa_length": 1511,
"cds_start": 3080,
"cds_end": null,
"cds_length": 4536,
"cdna_start": 3129,
"cdna_end": null,
"cdna_length": 5707,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3047A>G",
"hgvs_p": "p.Asn1016Ser",
"transcript": "NM_001122633.3",
"protein_id": "NP_001116105.2",
"transcript_support_level": null,
"aa_start": 1016,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3047,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 3144,
"cdna_end": null,
"cdna_length": 5722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3047A>G",
"hgvs_p": "p.Asn1016Ser",
"transcript": "NM_001369257.1",
"protein_id": "NP_001356186.1",
"transcript_support_level": null,
"aa_start": 1016,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3047,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 3264,
"cdna_end": null,
"cdna_length": 5842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3047A>G",
"hgvs_p": "p.Asn1016Ser",
"transcript": "ENST00000673510.1",
"protein_id": "ENSP00000500537.1",
"transcript_support_level": null,
"aa_start": 1016,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3047,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 3267,
"cdna_end": null,
"cdna_length": 4880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3047A>G",
"hgvs_p": "p.Asn1016Ser",
"transcript": "ENST00000673630.1",
"protein_id": "ENSP00000501073.1",
"transcript_support_level": null,
"aa_start": 1016,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3047,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 3381,
"cdna_end": null,
"cdna_length": 5775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "c.3047A>G",
"hgvs_p": "p.Asn1016Ser",
"transcript": "ENST00000673711.1",
"protein_id": "ENSP00000501022.1",
"transcript_support_level": null,
"aa_start": 1016,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3047,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 3120,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "n.419A>G",
"hgvs_p": null,
"transcript": "ENST00000497121.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 585,
"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": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "n.1526A>G",
"hgvs_p": null,
"transcript": "ENST00000673698.1",
"protein_id": "ENSP00000501214.1",
"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": 4138,
"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": 15,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "n.2192A>G",
"hgvs_p": null,
"transcript": "ENST00000674074.1",
"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": 4770,
"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": 26,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "n.3956A>G",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"hgvs_c": "n.2203A>G",
"hgvs_p": null,
"transcript": "NR_163592.1",
"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": 4781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CPS1",
"gene_hgnc_id": 2323,
"dbsnp": "rs749238466",
"frequency_reference_population": 0.0000024783578,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000205229,
"gnomad_genomes_af": 0.00000657082,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9378601312637329,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.892,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8741,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.606,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000233072.10",
"gene_symbol": "CPS1",
"hgnc_id": 2323,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3047A>G",
"hgvs_p": "p.Asn1016Ser"
}
],
"clinvar_disease": " type I,Congenital hyperammonemia",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Congenital hyperammonemia, type I",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}