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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: 2-72135413-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=72135413&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 72135413,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_019885.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.436T>C",
"hgvs_p": "p.Ser146Pro",
"transcript": "NM_019885.4",
"protein_id": "NP_063938.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 512,
"cds_start": 436,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000001146.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019885.4"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.436T>C",
"hgvs_p": "p.Ser146Pro",
"transcript": "ENST00000001146.7",
"protein_id": "ENSP00000001146.2",
"transcript_support_level": 1,
"aa_start": 146,
"aa_end": null,
"aa_length": 512,
"cds_start": 436,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_019885.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000001146.7"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.211T>C",
"hgvs_p": "p.Ser71Pro",
"transcript": "ENST00000546307.5",
"protein_id": "ENSP00000443304.1",
"transcript_support_level": 1,
"aa_start": 71,
"aa_end": null,
"aa_length": 437,
"cds_start": 211,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000546307.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.-138T>C",
"hgvs_p": null,
"transcript": "ENST00000412253.1",
"protein_id": "ENSP00000401465.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 321,
"cds_start": null,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000412253.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.211T>C",
"hgvs_p": "p.Ser71Pro",
"transcript": "NM_001277742.2",
"protein_id": "NP_001264671.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 437,
"cds_start": 211,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001277742.2"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.211T>C",
"hgvs_p": "p.Ser71Pro",
"transcript": "ENST00000474509.1",
"protein_id": "ENSP00000430888.1",
"transcript_support_level": 4,
"aa_start": 71,
"aa_end": null,
"aa_length": 181,
"cds_start": 211,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474509.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.385T>C",
"hgvs_p": "p.Ser129Pro",
"transcript": "ENST00000461519.1",
"protein_id": "ENSP00000430871.1",
"transcript_support_level": 3,
"aa_start": 129,
"aa_end": null,
"aa_length": 171,
"cds_start": 385,
"cds_end": null,
"cds_length": 518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000461519.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.262T>C",
"hgvs_p": "p.Ser88Pro",
"transcript": "XM_005264433.5",
"protein_id": "XP_005264490.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 454,
"cds_start": 262,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005264433.5"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.118T>C",
"hgvs_p": "p.Ser40Pro",
"transcript": "XM_047445119.1",
"protein_id": "XP_047301075.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 406,
"cds_start": 118,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445119.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.-138T>C",
"hgvs_p": null,
"transcript": "XM_011532988.2",
"protein_id": "XP_011531290.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 321,
"cds_start": null,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532988.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"hgvs_c": "c.-138T>C",
"hgvs_p": null,
"transcript": "XM_047445120.1",
"protein_id": "XP_047301076.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 321,
"cds_start": null,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445120.1"
}
],
"gene_symbol": "CYP26B1",
"gene_hgnc_id": 20581,
"dbsnp": "rs281875232",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8042917847633362,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.532,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.888,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.695,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_019885.4",
"gene_symbol": "CYP26B1",
"hgnc_id": 20581,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.436T>C",
"hgvs_p": "p.Ser146Pro"
}
],
"clinvar_disease": "Lethal occipital encephalocele-skeletal dysplasia syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Lethal occipital encephalocele-skeletal dysplasia syndrome|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}