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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: 2-189068105-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189068105&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 189068105,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_000393.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1311A>G",
"hgvs_p": "p.Pro437Pro",
"transcript": "NM_000393.5",
"protein_id": "NP_000384.2",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 1499,
"cds_start": 1311,
"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": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1311A>G",
"hgvs_p": "p.Pro437Pro",
"transcript": "ENST00000374866.9",
"protein_id": "ENSP00000364000.3",
"transcript_support_level": 1,
"aa_start": 437,
"aa_end": null,
"aa_length": 1499,
"cds_start": 1311,
"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": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1308A>G",
"hgvs_p": "p.Pro436Pro",
"transcript": "ENST00000858728.1",
"protein_id": "ENSP00000528787.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 1498,
"cds_start": 1308,
"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": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1311A>G",
"hgvs_p": "p.Pro437Pro",
"transcript": "ENST00000858729.1",
"protein_id": "ENSP00000528788.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 1463,
"cds_start": 1311,
"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": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Pro391Pro",
"transcript": "XM_011510573.4",
"protein_id": "XP_011508875.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 1453,
"cds_start": 1173,
"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": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Pro391Pro",
"transcript": "XM_047443251.1",
"protein_id": "XP_047299207.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 1453,
"cds_start": 1173,
"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": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1173A>G",
"hgvs_p": "p.Pro391Pro",
"transcript": "XM_047443252.1",
"protein_id": "XP_047299208.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 1453,
"cds_start": 1173,
"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"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.359-1672A>G",
"hgvs_p": null,
"transcript": "ENST00000618828.1",
"protein_id": "ENSP00000482184.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1112,
"cds_start": null,
"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"
}
],
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"dbsnp": "rs2229495",
"frequency_reference_population": 0.97371376,
"hom_count_reference_population": 765725,
"allele_count_reference_population": 1571276,
"gnomad_exomes_af": 0.975332,
"gnomad_genomes_af": 0.958171,
"gnomad_exomes_ac": 1425452,
"gnomad_genomes_ac": 145824,
"gnomad_exomes_homalt": 695771,
"gnomad_genomes_homalt": 69954,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"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": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -5.793,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000393.5",
"gene_symbol": "COL5A2",
"hgnc_id": 2210,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1311A>G",
"hgvs_p": "p.Pro437Pro"
}
],
"clinvar_disease": " 1, 2, classic type,Ehlers-Danlos syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "Ehlers-Danlos syndrome, classic type, 1|not specified|Ehlers-Danlos syndrome, classic type, 2|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}