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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: 22-42060109-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=42060109&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 42060109,
"ref": "C",
"alt": "T",
"effect": "3_prime_UTR_variant",
"transcript": "NM_000262.3",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "NM_000262.3",
"protein_id": "NP_000253.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": null,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000396398.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000262.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000396398.8",
"protein_id": "ENSP00000379680.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": null,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000262.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396398.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000898675.1",
"protein_id": "ENSP00000568734.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 446,
"cds_start": null,
"cds_end": null,
"cds_length": 1341,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898675.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "NM_001362848.1",
"protein_id": "NP_001349777.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": null,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001362848.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "NM_001362850.1",
"protein_id": "NP_001349779.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": null,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001362850.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000402937.1",
"protein_id": "ENSP00000384603.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": null,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000402937.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000403363.5",
"protein_id": "ENSP00000385283.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": null,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000403363.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000898674.1",
"protein_id": "ENSP00000568733.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": null,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898674.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000958241.1",
"protein_id": "ENSP00000628300.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": null,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958241.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000898671.1",
"protein_id": "ENSP00000568730.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 396,
"cds_start": null,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898671.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000898673.1",
"protein_id": "ENSP00000568732.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 380,
"cds_start": null,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898673.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"hgvs_c": "c.*170G>A",
"hgvs_p": null,
"transcript": "ENST00000898672.1",
"protein_id": "ENSP00000568731.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 357,
"cds_start": null,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898672.1"
}
],
"gene_symbol": "NAGA",
"gene_hgnc_id": 7631,
"dbsnp": "rs142863061",
"frequency_reference_population": 0.0015869812,
"hom_count_reference_population": 9,
"allele_count_reference_population": 1368,
"gnomad_exomes_af": 0.000687531,
"gnomad_genomes_af": 0.0057808,
"gnomad_exomes_ac": 488,
"gnomad_genomes_ac": 880,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 7,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.179,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000262.3",
"gene_symbol": "NAGA",
"hgnc_id": 7631,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*170G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Alpha-N-acetylgalactosaminidase deficiency type 1,Alpha-N-acetylgalactosaminidase deficiency type 2,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "Alpha-N-acetylgalactosaminidase deficiency type 1|Alpha-N-acetylgalactosaminidase deficiency type 2|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}