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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: 12-71578827-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=71578827&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 71578827,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000266674.10",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.1304C>T",
"hgvs_p": "p.Ser435Leu",
"transcript": "NM_003667.4",
"protein_id": "NP_003658.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 907,
"cds_start": 1304,
"cds_end": null,
"cds_length": 2724,
"cdna_start": 1587,
"cdna_end": null,
"cdna_length": 4583,
"mane_select": "ENST00000266674.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.1304C>T",
"hgvs_p": "p.Ser435Leu",
"transcript": "ENST00000266674.10",
"protein_id": "ENSP00000266674.4",
"transcript_support_level": 1,
"aa_start": 435,
"aa_end": null,
"aa_length": 907,
"cds_start": 1304,
"cds_end": null,
"cds_length": 2724,
"cdna_start": 1587,
"cdna_end": null,
"cdna_length": 4583,
"mane_select": "NM_003667.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.1232C>T",
"hgvs_p": "p.Ser411Leu",
"transcript": "ENST00000540815.2",
"protein_id": "ENSP00000441035.2",
"transcript_support_level": 1,
"aa_start": 411,
"aa_end": null,
"aa_length": 883,
"cds_start": 1232,
"cds_end": null,
"cds_length": 2652,
"cdna_start": 1278,
"cdna_end": null,
"cdna_length": 2800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.1088C>T",
"hgvs_p": "p.Ser363Leu",
"transcript": "ENST00000536515.5",
"protein_id": "ENSP00000443033.1",
"transcript_support_level": 1,
"aa_start": 363,
"aa_end": null,
"aa_length": 835,
"cds_start": 1088,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 1136,
"cdna_end": null,
"cdna_length": 2664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.1232C>T",
"hgvs_p": "p.Ser411Leu",
"transcript": "NM_001277226.2",
"protein_id": "NP_001264155.1",
"transcript_support_level": null,
"aa_start": 411,
"aa_end": null,
"aa_length": 883,
"cds_start": 1232,
"cds_end": null,
"cds_length": 2652,
"cdna_start": 1515,
"cdna_end": null,
"cdna_length": 4511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.1088C>T",
"hgvs_p": "p.Ser363Leu",
"transcript": "NM_001277227.2",
"protein_id": "NP_001264156.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 835,
"cds_start": 1088,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 1371,
"cdna_end": null,
"cdna_length": 4367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.1082C>T",
"hgvs_p": "p.Ser361Leu",
"transcript": "XM_047429800.1",
"protein_id": "XP_047285756.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 833,
"cds_start": 1082,
"cds_end": null,
"cds_length": 2502,
"cdna_start": 1283,
"cdna_end": null,
"cdna_length": 4279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "c.1016C>T",
"hgvs_p": "p.Ser339Leu",
"transcript": "XM_047429801.1",
"protein_id": "XP_047285757.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 811,
"cds_start": 1016,
"cds_end": null,
"cds_length": 2436,
"cdna_start": 1299,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "n.484C>T",
"hgvs_p": null,
"transcript": "ENST00000547310.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 576,
"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": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "n.1685C>T",
"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": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"hgvs_c": "n.1871C>T",
"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
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124902963",
"gene_hgnc_id": null,
"hgvs_c": "n.126-1796G>A",
"hgvs_p": null,
"transcript": "XR_007063365.1",
"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": 214,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LGR5",
"gene_hgnc_id": 4504,
"dbsnp": "rs73339868",
"frequency_reference_population": 0.00040938237,
"hom_count_reference_population": 1,
"allele_count_reference_population": 659,
"gnomad_exomes_af": 0.000257286,
"gnomad_genomes_af": 0.00186572,
"gnomad_exomes_ac": 375,
"gnomad_genomes_ac": 284,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011430352926254272,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.232,
"revel_prediction": "Benign",
"alphamissense_score": 0.1191,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.608,
"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,BP6_Very_Strong",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000266674.10",
"gene_symbol": "LGR5",
"hgnc_id": 4504,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1304C>T",
"hgvs_p": "p.Ser435Leu"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "XR_007063365.1",
"gene_symbol": "LOC124902963",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.126-1796G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}