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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: 2-189068226-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189068226&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"gene_symbol": "COL5A2",
"hgnc_id": 2210,
"hgvs_c": "c.1302G>A",
"hgvs_p": "p.Thr434Thr",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_000393.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 79,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "2",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 1, classic type,Ehlers-Danlos syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.49000000953674316,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1499,
"aa_ref": "T",
"aa_start": 434,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6829,
"cdna_start": 1459,
"cds_end": null,
"cds_length": 4500,
"cds_start": 1302,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_000393.5",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.1302G>A",
"hgvs_p": "p.Thr434Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374866.9",
"protein_coding": true,
"protein_id": "NP_000384.2",
"strand": false,
"transcript": "NM_000393.5",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1499,
"aa_ref": "T",
"aa_start": 434,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6829,
"cdna_start": 1459,
"cds_end": null,
"cds_length": 4500,
"cds_start": 1302,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000374866.9",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.1302G>A",
"hgvs_p": "p.Thr434Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000393.5",
"protein_coding": true,
"protein_id": "ENSP00000364000.3",
"strand": false,
"transcript": "ENST00000374866.9",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1498,
"aa_ref": "T",
"aa_start": 433,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5244,
"cdna_start": 1456,
"cds_end": null,
"cds_length": 4497,
"cds_start": 1299,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000858728.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.1299G>A",
"hgvs_p": "p.Thr433Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528787.1",
"strand": false,
"transcript": "ENST00000858728.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "T",
"aa_start": 434,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4861,
"cdna_start": 1459,
"cds_end": null,
"cds_length": 4392,
"cds_start": 1302,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 53,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000858729.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.1302G>A",
"hgvs_p": "p.Thr434Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528788.1",
"strand": false,
"transcript": "ENST00000858729.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1453,
"aa_ref": "T",
"aa_start": 388,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7124,
"cdna_start": 1754,
"cds_end": null,
"cds_length": 4362,
"cds_start": 1164,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 57,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_011510573.4",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.1164G>A",
"hgvs_p": "p.Thr388Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508875.1",
"strand": false,
"transcript": "XM_011510573.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1453,
"aa_ref": "T",
"aa_start": 388,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7296,
"cdna_start": 1926,
"cds_end": null,
"cds_length": 4362,
"cds_start": 1164,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 59,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "XM_047443251.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.1164G>A",
"hgvs_p": "p.Thr388Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299207.1",
"strand": false,
"transcript": "XM_047443251.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1453,
"aa_ref": "T",
"aa_start": 388,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7078,
"cdna_start": 1708,
"cds_end": null,
"cds_length": 4362,
"cds_start": 1164,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 58,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_047443252.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.1164G>A",
"hgvs_p": "p.Thr388Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299208.1",
"strand": false,
"transcript": "XM_047443252.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1112,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6399,
"cdna_start": null,
"cds_end": null,
"cds_length": 3339,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 47,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000618828.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.359-1793G>A",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000482184.1",
"strand": false,
"transcript": "ENST00000618828.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.702028226379161,
"dbsnp": "rs376170776",
"effect": "splice_region_variant,synonymous_variant",
"frequency_reference_population": 0.00004895982,
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"gnomad_exomes_ac": 77,
"gnomad_exomes_af": 0.0000526875,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131475,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Ehlers-Danlos syndrome, classic type, 1|not provided|not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.618,
"pos": 189068226,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.6620000004768372,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.08,
"transcript": "NM_000393.5"
}
]
}