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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: 1-52374887-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=52374887&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 52374887,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000371568.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.2314G>A",
"hgvs_p": "p.Val772Ile",
"transcript": "NM_004153.4",
"protein_id": "NP_004144.2",
"transcript_support_level": null,
"aa_start": 772,
"aa_end": null,
"aa_length": 861,
"cds_start": 2314,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2497,
"cdna_end": null,
"cdna_length": 3121,
"mane_select": "ENST00000371568.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.2314G>A",
"hgvs_p": "p.Val772Ile",
"transcript": "ENST00000371568.8",
"protein_id": "ENSP00000360623.3",
"transcript_support_level": 1,
"aa_start": 772,
"aa_end": null,
"aa_length": 861,
"cds_start": 2314,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2497,
"cdna_end": null,
"cdna_length": 3121,
"mane_select": "NM_004153.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.2314G>A",
"hgvs_p": "p.Val772Ile",
"transcript": "ENST00000371566.1",
"protein_id": "ENSP00000360621.1",
"transcript_support_level": 1,
"aa_start": 772,
"aa_end": null,
"aa_length": 861,
"cds_start": 2314,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2458,
"cdna_end": null,
"cdna_length": 3080,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.2314G>A",
"hgvs_p": "p.Val772Ile",
"transcript": "NM_001190818.2",
"protein_id": "NP_001177747.1",
"transcript_support_level": null,
"aa_start": 772,
"aa_end": null,
"aa_length": 861,
"cds_start": 2314,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2494,
"cdna_end": null,
"cdna_length": 3118,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.2299G>A",
"hgvs_p": "p.Val767Ile",
"transcript": "NM_001190819.2",
"protein_id": "NP_001177748.1",
"transcript_support_level": null,
"aa_start": 767,
"aa_end": null,
"aa_length": 856,
"cds_start": 2299,
"cds_end": null,
"cds_length": 2571,
"cdna_start": 2482,
"cdna_end": null,
"cdna_length": 3106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.2314G>A",
"hgvs_p": "p.Val772Ile",
"transcript": "XM_047421674.1",
"protein_id": "XP_047277630.1",
"transcript_support_level": null,
"aa_start": 772,
"aa_end": null,
"aa_length": 861,
"cds_start": 2314,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2490,
"cdna_end": null,
"cdna_length": 3114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.2206G>A",
"hgvs_p": "p.Val736Ile",
"transcript": "XM_017001388.3",
"protein_id": "XP_016856877.1",
"transcript_support_level": null,
"aa_start": 736,
"aa_end": null,
"aa_length": 825,
"cds_start": 2206,
"cds_end": null,
"cds_length": 2478,
"cdna_start": 2389,
"cdna_end": null,
"cdna_length": 3013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.2206G>A",
"hgvs_p": "p.Val736Ile",
"transcript": "XM_047421680.1",
"protein_id": "XP_047277636.1",
"transcript_support_level": null,
"aa_start": 736,
"aa_end": null,
"aa_length": 825,
"cds_start": 2206,
"cds_end": null,
"cds_length": 2478,
"cdna_start": 2386,
"cdna_end": null,
"cdna_length": 3010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"hgvs_c": "c.1234G>A",
"hgvs_p": "p.Val412Ile",
"transcript": "XM_011541527.4",
"protein_id": "XP_011539829.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 501,
"cds_start": 1234,
"cds_end": null,
"cds_length": 1506,
"cdna_start": 1650,
"cdna_end": null,
"cdna_length": 2274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ORC1",
"gene_hgnc_id": 8487,
"dbsnp": "rs61753389",
"frequency_reference_population": 0.0057939813,
"hom_count_reference_population": 40,
"allele_count_reference_population": 9344,
"gnomad_exomes_af": 0.00590239,
"gnomad_genomes_af": 0.00475434,
"gnomad_exomes_ac": 8620,
"gnomad_genomes_ac": 724,
"gnomad_exomes_homalt": 39,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006574392318725586,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.047,
"revel_prediction": "Benign",
"alphamissense_score": 0.0677,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.016,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000371568.8",
"gene_symbol": "ORC1",
"hgnc_id": 8487,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2314G>A",
"hgvs_p": "p.Val772Ile"
}
],
"clinvar_disease": "Meier-Gorlin syndrome 1,ORC1-related disorder,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:2 O:1",
"phenotype_combined": "not specified|not provided|Meier-Gorlin syndrome 1|ORC1-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}