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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: 1-207454430-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=207454430&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 207454430,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001006658.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"hgvs_c": "c.12G>A",
"hgvs_p": "p.Ala4Ala",
"transcript": "NM_001006658.3",
"protein_id": "NP_001006659.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 1092,
"cds_start": 12,
"cds_end": null,
"cds_length": 3279,
"cdna_start": 103,
"cdna_end": null,
"cdna_length": 4139,
"mane_select": "ENST00000367057.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"hgvs_c": "c.12G>A",
"hgvs_p": "p.Ala4Ala",
"transcript": "ENST00000367057.8",
"protein_id": "ENSP00000356024.3",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 1092,
"cds_start": 12,
"cds_end": null,
"cds_length": 3279,
"cdna_start": 103,
"cdna_end": null,
"cdna_length": 4139,
"mane_select": "NM_001006658.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"hgvs_c": "c.12G>A",
"hgvs_p": "p.Ala4Ala",
"transcript": "ENST00000367058.7",
"protein_id": "ENSP00000356025.3",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 1033,
"cds_start": 12,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 4063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"hgvs_c": "c.12G>A",
"hgvs_p": "p.Ala4Ala",
"transcript": "ENST00000367059.3",
"protein_id": "ENSP00000356026.3",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 971,
"cds_start": 12,
"cds_end": null,
"cds_length": 2916,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 3877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"hgvs_c": "c.12G>A",
"hgvs_p": "p.Ala4Ala",
"transcript": "NM_001877.5",
"protein_id": "NP_001868.2",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 1033,
"cds_start": 12,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 103,
"cdna_end": null,
"cdna_length": 3962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"hgvs_c": "c.-431G>A",
"hgvs_p": null,
"transcript": "ENST00000699620.1",
"protein_id": "ENSP00000514480.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 910,
"cds_start": -4,
"cds_end": null,
"cds_length": 2733,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"hgvs_c": "c.-385+1335G>A",
"hgvs_p": null,
"transcript": "ENST00000699640.1",
"protein_id": "ENSP00000514493.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 27,
"cds_start": -4,
"cds_end": null,
"cds_length": 86,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"hgvs_c": "n.-221G>A",
"hgvs_p": null,
"transcript": "ENST00000479186.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CR2",
"gene_hgnc_id": 2336,
"dbsnp": "rs1478924012",
"frequency_reference_population": 0.000022096685,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000209533,
"gnomad_genomes_af": 0.0000328537,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"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": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.015,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_001006658.3",
"gene_symbol": "CR2",
"hgnc_id": 2336,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown,AR,AD",
"hgvs_c": "c.12G>A",
"hgvs_p": "p.Ala4Ala"
}
],
"clinvar_disease": " 7, common variable,Immunodeficiency",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Immunodeficiency, common variable, 7",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}