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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: 11-46857966-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=46857966&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 46857966,
"ref": "G",
"alt": "A",
"effect": "3_prime_UTR_variant",
"transcript": "NM_002334.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.*1017C>T",
"hgvs_p": null,
"transcript": "NM_002334.4",
"protein_id": "NP_002325.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1905,
"cds_start": null,
"cds_end": null,
"cds_length": 5718,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000378623.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002334.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.*1017C>T",
"hgvs_p": null,
"transcript": "ENST00000378623.6",
"protein_id": "ENSP00000367888.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1905,
"cds_start": null,
"cds_end": null,
"cds_length": 5718,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002334.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378623.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.*1017C>T",
"hgvs_p": null,
"transcript": "ENST00000858258.1",
"protein_id": "ENSP00000528317.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1722,
"cds_start": null,
"cds_end": null,
"cds_length": 5169,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858258.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.*1367C>T",
"hgvs_p": null,
"transcript": "XM_017017734.2",
"protein_id": "XP_016873223.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1809,
"cds_start": null,
"cds_end": null,
"cds_length": 5430,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017017734.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.*1017C>T",
"hgvs_p": null,
"transcript": "XM_011520103.3",
"protein_id": "XP_011518405.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1637,
"cds_start": null,
"cds_end": null,
"cds_length": 4914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520103.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.*1017C>T",
"hgvs_p": null,
"transcript": "XM_011520104.3",
"protein_id": "XP_011518406.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1160,
"cds_start": null,
"cds_end": null,
"cds_length": 3483,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520104.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "n.1678C>T",
"hgvs_p": null,
"transcript": "ENST00000529604.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000529604.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LRP4-AS1",
"gene_hgnc_id": 44128,
"hgvs_c": "n.196+11249G>A",
"hgvs_p": null,
"transcript": "ENST00000502049.4",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000502049.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LRP4-AS1",
"gene_hgnc_id": 44128,
"hgvs_c": "n.291+5020G>A",
"hgvs_p": null,
"transcript": "ENST00000531719.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000531719.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LRP4-AS1",
"gene_hgnc_id": 44128,
"hgvs_c": "n.197+11249G>A",
"hgvs_p": null,
"transcript": "NR_038909.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_038909.1"
}
],
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"dbsnp": "rs10838623",
"frequency_reference_population": 0.010790469,
"hom_count_reference_population": 229,
"allele_count_reference_population": 1643,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.0107905,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 1643,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 229,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8199999928474426,
"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": -0.82,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.444,
"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,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_002334.4",
"gene_symbol": "LRP4",
"hgnc_id": 6696,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR,SD",
"hgvs_c": "c.*1017C>T",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000502049.4",
"gene_symbol": "LRP4-AS1",
"hgnc_id": 44128,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.196+11249G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Cenani-Lenz syndactyly syndrome,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Cenani-Lenz syndactyly syndrome|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}