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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: 10-119912139-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=119912139&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 119912139,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000369075.8",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "c.1287T>A",
"hgvs_p": "p.Asp429Glu",
"transcript": "NM_007190.4",
"protein_id": "NP_009121.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 1000,
"cds_start": 1287,
"cds_end": null,
"cds_length": 3003,
"cdna_start": 1340,
"cdna_end": null,
"cdna_length": 7148,
"mane_select": "ENST00000369075.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "c.1287T>A",
"hgvs_p": "p.Asp429Glu",
"transcript": "ENST00000369075.8",
"protein_id": "ENSP00000358071.3",
"transcript_support_level": 1,
"aa_start": 429,
"aa_end": null,
"aa_length": 1000,
"cds_start": 1287,
"cds_end": null,
"cds_length": 3003,
"cdna_start": 1340,
"cdna_end": null,
"cdna_length": 7148,
"mane_select": "NM_007190.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "c.1287T>A",
"hgvs_p": "p.Asp429Glu",
"transcript": "NM_001411070.1",
"protein_id": "NP_001397999.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 999,
"cds_start": 1287,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 1340,
"cdna_end": null,
"cdna_length": 7145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "c.1287T>A",
"hgvs_p": "p.Asp429Glu",
"transcript": "ENST00000705471.1",
"protein_id": "ENSP00000516127.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 999,
"cds_start": 1287,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 1363,
"cdna_end": null,
"cdna_length": 4613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "c.399T>A",
"hgvs_p": "p.Asp133Glu",
"transcript": "ENST00000446561.1",
"protein_id": "ENSP00000396906.1",
"transcript_support_level": 3,
"aa_start": 133,
"aa_end": null,
"aa_length": 193,
"cds_start": 399,
"cds_end": null,
"cds_length": 582,
"cdna_start": 399,
"cdna_end": null,
"cdna_length": 582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "c.1287T>A",
"hgvs_p": "p.Asp429Glu",
"transcript": "XM_047424537.1",
"protein_id": "XP_047280493.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 1000,
"cds_start": 1287,
"cds_end": null,
"cds_length": 3003,
"cdna_start": 1340,
"cdna_end": null,
"cdna_length": 3127,
"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": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "n.807T>A",
"hgvs_p": null,
"transcript": "NR_037771.2",
"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": 6615,
"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": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "n.1340T>A",
"hgvs_p": null,
"transcript": "XR_007061940.1",
"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": 4315,
"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": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"hgvs_c": "n.1340T>A",
"hgvs_p": null,
"transcript": "XR_246061.3",
"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": 4318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SEC23IP",
"gene_hgnc_id": 17018,
"dbsnp": "rs17099368",
"frequency_reference_population": 0.0000013681912,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136819,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.26600298285484314,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.301,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2064,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.018,
"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": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000369075.8",
"gene_symbol": "SEC23IP",
"hgnc_id": 17018,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1287T>A",
"hgvs_p": "p.Asp429Glu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}