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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: 7-27165112-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=27165112&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 27165112,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_152739.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Pro116Ser",
"transcript": "NM_152739.4",
"protein_id": "NP_689952.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 272,
"cds_start": 346,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000343483.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152739.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Pro116Ser",
"transcript": "ENST00000343483.7",
"protein_id": "ENSP00000343619.6",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 272,
"cds_start": 346,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152739.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000343483.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXA10-HOXA9",
"gene_hgnc_id": 51908,
"hgvs_c": "c.11-145C>T",
"hgvs_p": null,
"transcript": "ENST00000470747.5",
"protein_id": "ENSP00000421799.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 112,
"cds_start": null,
"cds_end": null,
"cds_length": 339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000470747.5"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "n.480-1271C>T",
"hgvs_p": null,
"transcript": "ENST00000465941.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000465941.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "n.152-1271C>T",
"hgvs_p": null,
"transcript": "ENST00000497089.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000497089.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Pro116Ser",
"transcript": "ENST00000673744.1",
"protein_id": "ENSP00000500958.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 225,
"cds_start": 346,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000673744.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "c.313+33C>T",
"hgvs_p": null,
"transcript": "ENST00000673917.1",
"protein_id": "ENSP00000501229.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 213,
"cds_start": null,
"cds_end": null,
"cds_length": 642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000673917.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXA10-HOXA9",
"gene_hgnc_id": 51908,
"hgvs_c": "c.11-145C>T",
"hgvs_p": null,
"transcript": "NM_001433944.1",
"protein_id": "NP_001420873.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 112,
"cds_start": null,
"cds_end": null,
"cds_length": 339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001433944.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "c.317+29C>T",
"hgvs_p": null,
"transcript": "ENST00000396345.1",
"protein_id": "ENSP00000379634.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 106,
"cds_start": null,
"cds_end": null,
"cds_length": 321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396345.1"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "n.69-145C>T",
"hgvs_p": null,
"transcript": "ENST00000487384.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000487384.5"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"hgvs_c": "n.272-145C>T",
"hgvs_p": null,
"transcript": "ENST00000489695.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000489695.1"
}
],
"gene_symbol": "HOXA9",
"gene_hgnc_id": 5109,
"dbsnp": "rs771025386",
"frequency_reference_population": 6.8534274e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.85343e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.333577036857605,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.377,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0743,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.46,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_152739.4",
"gene_symbol": "HOXA9",
"hgnc_id": 5109,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Pro116Ser"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001433944.1",
"gene_symbol": "HOXA10-HOXA9",
"hgnc_id": 51908,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.11-145C>T",
"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
}