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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: 12-71556627-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=71556627&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 71556627,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003667.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.653A>C",
"hgvs_p": "p.His218Pro",
"transcript": "NM_003667.4",
"protein_id": "NP_003658.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 907,
"cds_start": 653,
"cds_end": null,
"cds_length": 2724,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000266674.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003667.4"
},
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.653A>C",
"hgvs_p": "p.His218Pro",
"transcript": "ENST00000266674.10",
"protein_id": "ENSP00000266674.4",
"transcript_support_level": 1,
"aa_start": 218,
"aa_end": null,
"aa_length": 907,
"cds_start": 653,
"cds_end": null,
"cds_length": 2724,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003667.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000266674.10"
},
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.653A>C",
"hgvs_p": "p.His218Pro",
"transcript": "ENST00000540815.2",
"protein_id": "ENSP00000441035.2",
"transcript_support_level": 1,
"aa_start": 218,
"aa_end": null,
"aa_length": 883,
"cds_start": 653,
"cds_end": null,
"cds_length": 2652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540815.2"
},
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.437A>C",
"hgvs_p": "p.His146Pro",
"transcript": "ENST00000536515.5",
"protein_id": "ENSP00000443033.1",
"transcript_support_level": 1,
"aa_start": 146,
"aa_end": null,
"aa_length": 835,
"cds_start": 437,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000536515.5"
},
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.653A>C",
"hgvs_p": "p.His218Pro",
"transcript": "NM_001277226.2",
"protein_id": "NP_001264155.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 883,
"cds_start": 653,
"cds_end": null,
"cds_length": 2652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001277226.2"
},
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.581A>C",
"hgvs_p": "p.His194Pro",
"transcript": "ENST00000856957.1",
"protein_id": "ENSP00000527016.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 883,
"cds_start": 581,
"cds_end": null,
"cds_length": 2652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856957.1"
},
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.437A>C",
"hgvs_p": "p.His146Pro",
"transcript": "NM_001277227.2",
"protein_id": "NP_001264156.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 835,
"cds_start": 437,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001277227.2"
},
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.431A>C",
"hgvs_p": "p.His144Pro",
"transcript": "XM_047429800.1",
"protein_id": "XP_047285756.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 833,
"cds_start": 431,
"cds_end": null,
"cds_length": 2502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429800.1"
},
{
"aa_ref": "H",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.437A>C",
"hgvs_p": "p.His146Pro",
"transcript": "XM_047429801.1",
"protein_id": "XP_047285757.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 811,
"cds_start": 437,
"cds_end": null,
"cds_length": 2436,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429801.1"
},
{
"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": 16,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.429-2959A>C",
"hgvs_p": null,
"transcript": "ENST00000856956.1",
"protein_id": "ENSP00000527015.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 811,
"cds_start": null,
"cds_end": null,
"cds_length": 2436,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856956.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "n.750A>C",
"hgvs_p": null,
"transcript": "ENST00000550851.5",
"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": "ENST00000550851.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "n.936A>C",
"hgvs_p": null,
"transcript": "NR_110596.2",
"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_110596.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC105369833",
"gene_hgnc_id": null,
"hgvs_c": "n.118+15006T>G",
"hgvs_p": null,
"transcript": "XR_001749200.2",
"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": "XR_001749200.2"
}
],
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"dbsnp": "rs117535164",
"frequency_reference_population": 0.0000065705613,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657056,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.820258378982544,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.466,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9379,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.22,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003667.4",
"gene_symbol": "LGR5",
"hgnc_id": 4504,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.653A>C",
"hgvs_p": "p.His218Pro"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "XR_001749200.2",
"gene_symbol": "LOC105369833",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.118+15006T>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}