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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: 10-87965473-A-ATTTT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=87965473&ref=A&alt=ATTTT&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 87965473,
"ref": "A",
"alt": "ATTTT",
"effect": "3_prime_UTR_variant",
"transcript": "NM_000314.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.*7_*10dupTTTT",
"hgvs_p": null,
"transcript": "NM_000314.8",
"protein_id": "NP_000305.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 403,
"cds_start": -4,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8515,
"mane_select": "ENST00000371953.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.*7_*10dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000371953.8",
"protein_id": "ENSP00000361021.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 403,
"cds_start": -4,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8515,
"mane_select": "NM_000314.8",
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*805_*808dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000686459.1",
"protein_id": "ENSP00000508909.1",
"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": 2712,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.1954_1957dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000688158.2",
"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": 8405,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*1049_*1052dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000688922.2",
"protein_id": "ENSP00000508742.2",
"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": 2818,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*558_*561dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000700022.1",
"protein_id": "ENSP00000514758.1",
"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": 2794,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.2377_2380dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000700023.1",
"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": 2428,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.2611_2614dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000700024.1",
"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": 4002,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*1254_*1257dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000706955.1",
"protein_id": "ENSP00000516675.1",
"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": 8685,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*248_*251dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000710265.1",
"protein_id": "ENSP00000518161.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 8579,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*1132_*1135dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000713837.1",
"protein_id": "ENSP00000519142.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
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"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "PTEN",
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"hgvs_c": "c.*7_*10dupTTTT",
"hgvs_p": null,
"transcript": "NM_001304717.5",
"protein_id": "NP_001291646.4",
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
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"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
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"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "PTEN",
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"hgvs_c": "c.*7_*10dupTTTT",
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"transcript": "ENST00000693560.1",
"protein_id": "ENSP00000509861.1",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": 10,
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"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "PTEN",
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},
{
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"strand": true,
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],
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"intron_rank": null,
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"gene_symbol": "PTEN",
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"transcript": "ENST00000713839.1",
"protein_id": "ENSP00000519144.1",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": 10,
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"intron_rank": null,
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"gene_symbol": "PTEN",
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},
{
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],
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"gene_symbol": "PTEN",
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"transcript": "ENST00000700021.1",
"protein_id": "ENSP00000514757.1",
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},
{
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"protein_coding": true,
"strand": true,
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],
"exon_rank": 9,
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"exon_count": 9,
"intron_rank": null,
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"gene_symbol": "PTEN",
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"hgvs_c": "c.*7_*10dupTTTT",
"hgvs_p": null,
"transcript": "NM_001304718.2",
"protein_id": "NP_001291647.1",
"transcript_support_level": null,
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "PTEN",
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"hgvs_c": "n.*805_*808dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000686459.1",
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},
{
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],
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"gene_symbol": "PTEN",
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"transcript": "ENST00000688922.2",
"protein_id": "ENSP00000508742.2",
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},
{
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"strand": true,
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],
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"intron_rank": null,
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"gene_symbol": "PTEN",
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*1254_*1257dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000706955.1",
"protein_id": "ENSP00000516675.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*248_*251dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000710265.1",
"protein_id": "ENSP00000518161.1",
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"cdna_length": 8579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*1132_*1135dupTTTT",
"hgvs_p": null,
"transcript": "ENST00000713837.1",
"protein_id": "ENSP00000519142.1",
"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": 8680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"dbsnp": "rs756681683",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 6.86708e-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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.096,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"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,BP6",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000314.8",
"gene_symbol": "PTEN",
"hgnc_id": 9588,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.*7_*10dupTTTT",
"hgvs_p": null
}
],
"clinvar_disease": "Cowden syndrome 1,Hereditary cancer-predisposing syndrome",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:1",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|Cowden syndrome 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}