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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: 12-71584663-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=71584663&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 71584663,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000266674.10",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.2653G>A",
"hgvs_p": "p.Val885Met",
"transcript": "NM_003667.4",
"protein_id": "NP_003658.1",
"transcript_support_level": null,
"aa_start": 885,
"aa_end": null,
"aa_length": 907,
"cds_start": 2653,
"cds_end": null,
"cds_length": 2724,
"cdna_start": 2936,
"cdna_end": null,
"cdna_length": 4583,
"mane_select": "ENST00000266674.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.2653G>A",
"hgvs_p": "p.Val885Met",
"transcript": "ENST00000266674.10",
"protein_id": "ENSP00000266674.4",
"transcript_support_level": 1,
"aa_start": 885,
"aa_end": null,
"aa_length": 907,
"cds_start": 2653,
"cds_end": null,
"cds_length": 2724,
"cdna_start": 2936,
"cdna_end": null,
"cdna_length": 4583,
"mane_select": "NM_003667.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.2581G>A",
"hgvs_p": "p.Val861Met",
"transcript": "ENST00000540815.2",
"protein_id": "ENSP00000441035.2",
"transcript_support_level": 1,
"aa_start": 861,
"aa_end": null,
"aa_length": 883,
"cds_start": 2581,
"cds_end": null,
"cds_length": 2652,
"cdna_start": 2627,
"cdna_end": null,
"cdna_length": 2800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.2437G>A",
"hgvs_p": "p.Val813Met",
"transcript": "ENST00000536515.5",
"protein_id": "ENSP00000443033.1",
"transcript_support_level": 1,
"aa_start": 813,
"aa_end": null,
"aa_length": 835,
"cds_start": 2437,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 2485,
"cdna_end": null,
"cdna_length": 2664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.2581G>A",
"hgvs_p": "p.Val861Met",
"transcript": "NM_001277226.2",
"protein_id": "NP_001264155.1",
"transcript_support_level": null,
"aa_start": 861,
"aa_end": null,
"aa_length": 883,
"cds_start": 2581,
"cds_end": null,
"cds_length": 2652,
"cdna_start": 2864,
"cdna_end": null,
"cdna_length": 4511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.2437G>A",
"hgvs_p": "p.Val813Met",
"transcript": "NM_001277227.2",
"protein_id": "NP_001264156.1",
"transcript_support_level": null,
"aa_start": 813,
"aa_end": null,
"aa_length": 835,
"cds_start": 2437,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 2720,
"cdna_end": null,
"cdna_length": 4367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.2431G>A",
"hgvs_p": "p.Val811Met",
"transcript": "XM_047429800.1",
"protein_id": "XP_047285756.1",
"transcript_support_level": null,
"aa_start": 811,
"aa_end": null,
"aa_length": 833,
"cds_start": 2431,
"cds_end": null,
"cds_length": 2502,
"cdna_start": 2632,
"cdna_end": null,
"cdna_length": 4279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.2365G>A",
"hgvs_p": "p.Val789Met",
"transcript": "XM_047429801.1",
"protein_id": "XP_047285757.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 811,
"cds_start": 2365,
"cds_end": null,
"cds_length": 2436,
"cdna_start": 2648,
"cdna_end": null,
"cdna_length": 4295,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "n.2452G>A",
"hgvs_p": null,
"transcript": "ENST00000550851.5",
"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": 4095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "n.2638G>A",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"dbsnp": "rs61737422",
"frequency_reference_population": 0.0019174914,
"hom_count_reference_population": 46,
"allele_count_reference_population": 3095,
"gnomad_exomes_af": 0.0010644,
"gnomad_genomes_af": 0.0101097,
"gnomad_exomes_ac": 1556,
"gnomad_genomes_ac": 1539,
"gnomad_exomes_homalt": 27,
"gnomad_genomes_homalt": 19,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.002332031726837158,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.03,
"revel_prediction": "Benign",
"alphamissense_score": 0.0848,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.037,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000266674.10",
"gene_symbol": "LGR5",
"hgnc_id": 4504,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2653G>A",
"hgvs_p": "p.Val885Met"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}