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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: 2-189039507-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189039507&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 189039507,
"ref": "T",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_000393.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.3690A>T",
"hgvs_p": "p.Thr1230Thr",
"transcript": "NM_000393.5",
"protein_id": "NP_000384.2",
"transcript_support_level": null,
"aa_start": 1230,
"aa_end": null,
"aa_length": 1499,
"cds_start": 3690,
"cds_end": null,
"cds_length": 4500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000374866.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000393.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.3690A>T",
"hgvs_p": "p.Thr1230Thr",
"transcript": "ENST00000374866.9",
"protein_id": "ENSP00000364000.3",
"transcript_support_level": 1,
"aa_start": 1230,
"aa_end": null,
"aa_length": 1499,
"cds_start": 3690,
"cds_end": null,
"cds_length": 4500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000393.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374866.9"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.3687A>T",
"hgvs_p": "p.Thr1229Thr",
"transcript": "ENST00000858728.1",
"protein_id": "ENSP00000528787.1",
"transcript_support_level": null,
"aa_start": 1229,
"aa_end": null,
"aa_length": 1498,
"cds_start": 3687,
"cds_end": null,
"cds_length": 4497,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858728.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.3582A>T",
"hgvs_p": "p.Thr1194Thr",
"transcript": "ENST00000858729.1",
"protein_id": "ENSP00000528788.1",
"transcript_support_level": null,
"aa_start": 1194,
"aa_end": null,
"aa_length": 1463,
"cds_start": 3582,
"cds_end": null,
"cds_length": 4392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858729.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.2529A>T",
"hgvs_p": "p.Thr843Thr",
"transcript": "ENST00000618828.1",
"protein_id": "ENSP00000482184.1",
"transcript_support_level": 5,
"aa_start": 843,
"aa_end": null,
"aa_length": 1112,
"cds_start": 2529,
"cds_end": null,
"cds_length": 3339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000618828.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.3552A>T",
"hgvs_p": "p.Thr1184Thr",
"transcript": "XM_011510573.4",
"protein_id": "XP_011508875.1",
"transcript_support_level": null,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1453,
"cds_start": 3552,
"cds_end": null,
"cds_length": 4362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510573.4"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.3552A>T",
"hgvs_p": "p.Thr1184Thr",
"transcript": "XM_047443251.1",
"protein_id": "XP_047299207.1",
"transcript_support_level": null,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1453,
"cds_start": 3552,
"cds_end": null,
"cds_length": 4362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443251.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.3552A>T",
"hgvs_p": "p.Thr1184Thr",
"transcript": "XM_047443252.1",
"protein_id": "XP_047299208.1",
"transcript_support_level": null,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1453,
"cds_start": 3552,
"cds_end": null,
"cds_length": 4362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443252.1"
}
],
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"dbsnp": "rs10197596",
"frequency_reference_population": 0.000002052374,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205237,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5099999904632568,
"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": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.989,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 13,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_000393.5",
"gene_symbol": "COL5A2",
"hgnc_id": 2210,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3690A>T",
"hgvs_p": "p.Thr1230Thr"
}
],
"clinvar_disease": " 1, classic type,Ehlers-Danlos syndrome,Familial thoracic aortic aneurysm and aortic dissection",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Ehlers-Danlos syndrome, classic type, 1|Familial thoracic aortic aneurysm and aortic dissection",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}