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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: 3-8733893-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=8733893&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 8733893,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_033337.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "c.17A>G",
"hgvs_p": "p.His6Arg",
"transcript": "NM_033337.3",
"protein_id": "NP_203123.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 151,
"cds_start": 17,
"cds_end": null,
"cds_length": 456,
"cdna_start": 92,
"cdna_end": null,
"cdna_length": 1422,
"mane_select": "ENST00000343849.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "c.17A>G",
"hgvs_p": "p.His6Arg",
"transcript": "ENST00000343849.3",
"protein_id": "ENSP00000341940.2",
"transcript_support_level": 1,
"aa_start": 6,
"aa_end": null,
"aa_length": 151,
"cds_start": 17,
"cds_end": null,
"cds_length": 456,
"cdna_start": 92,
"cdna_end": null,
"cdna_length": 1422,
"mane_select": "NM_033337.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "c.17A>G",
"hgvs_p": "p.His6Arg",
"transcript": "ENST00000397368.2",
"protein_id": "ENSP00000380525.2",
"transcript_support_level": 1,
"aa_start": 6,
"aa_end": null,
"aa_length": 151,
"cds_start": 17,
"cds_end": null,
"cds_length": 456,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 1260,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SSUH2",
"gene_hgnc_id": 24809,
"hgvs_c": "n.335+8566T>C",
"hgvs_p": null,
"transcript": "ENST00000478513.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 1185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "c.17A>G",
"hgvs_p": "p.His6Arg",
"transcript": "NM_001234.5",
"protein_id": "NP_001225.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 151,
"cds_start": 17,
"cds_end": null,
"cds_length": 456,
"cdna_start": 92,
"cdna_end": null,
"cdna_length": 1326,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"hgvs_c": "n.58A>G",
"hgvs_p": null,
"transcript": "ENST00000472766.1",
"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": 680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 18,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SSUH2",
"gene_hgnc_id": 24809,
"hgvs_c": "c.-1126+8566T>C",
"hgvs_p": null,
"transcript": "ENST00000435138.5",
"protein_id": "ENSP00000412333.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 302,
"cds_start": -4,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CAV3",
"gene_hgnc_id": 1529,
"dbsnp": "rs1233979640",
"frequency_reference_population": 0.000013145095,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131451,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0629444420337677,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.259,
"revel_prediction": "Benign",
"alphamissense_score": 0.0621,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.166,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,PP2,BP4_Strong",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 4,
"pathogenic_score": 5,
"criteria": [
"PM1",
"PM2",
"PP2",
"BP4_Strong"
],
"verdict": "Uncertain_significance",
"transcript": "NM_033337.3",
"gene_symbol": "CAV3",
"hgnc_id": 1529,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.17A>G",
"hgvs_p": "p.His6Arg"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000478513.1",
"gene_symbol": "SSUH2",
"hgnc_id": 24809,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.335+8566T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Cardiovascular phenotype",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Cardiovascular phenotype",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}