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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: 3-167699151-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=167699151&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 167699151,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000392750.7",
"consequences": [
{
"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": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "NM_007217.4",
"protein_id": "NP_009148.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2133,
"mane_select": "ENST00000392750.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "ENST00000392750.7",
"protein_id": "ENSP00000376506.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2133,
"mane_select": "NM_007217.4",
"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": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "ENST00000473645.6",
"protein_id": "ENSP00000418317.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1360,
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "ENST00000497056.6",
"protein_id": "ENSP00000420553.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1276,
"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": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "NM_001439202.1",
"protein_id": "NP_001426131.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1984,
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "NM_001439204.1",
"protein_id": "NP_001426133.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1821,
"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": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "NM_001439205.1",
"protein_id": "NP_001426134.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1867,
"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": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "NM_145859.2",
"protein_id": "NP_665858.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1925,
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "NM_145860.2",
"protein_id": "NP_665859.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 8,
"intron_rank": 3,
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"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
"hgvs_p": null,
"transcript": "ENST00000461494.5",
"protein_id": "ENSP00000420021.1",
"transcript_support_level": 3,
"aa_start": null,
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"aa_length": 212,
"cds_start": -4,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 9,
"intron_rank": 4,
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"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"hgvs_c": "c.151-2025A>G",
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"transcript": "ENST00000470131.5",
"protein_id": "ENSP00000417202.1",
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},
{
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],
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},
{
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],
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"gene_symbol": "PDCD10",
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],
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"gene_symbol": "PDCD10",
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],
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},
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],
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"transcript": "ENST00000492139.5",
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},
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],
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"gene_symbol": "PDCD10",
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"hgvs_c": "c.91-2025A>G",
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"transcript": "ENST00000479121.5",
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},
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"exon_rank": null,
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"intron_rank": 5,
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"gene_symbol": "PDCD10",
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"hgvs_c": "c.151-2025A>G",
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"transcript": "ENST00000464360.5",
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],
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},
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],
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"intron_rank": 4,
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"gene_symbol": "PDCD10",
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"hgvs_c": "c.151-2025A>G",
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"protein_id": "XP_005247144.1",
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"feature": null
},
{
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"consequences": [
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],
"exon_rank": null,
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"exon_count": 10,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PDCD10",
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"hgvs_c": "c.151-2025A>G",
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"protein_id": "XP_011510670.1",
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"feature": null
},
{
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],
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},
{
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],
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"gene_symbol": "PDCD10",
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"transcript": "XM_047447374.1",
"protein_id": "XP_047303330.1",
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},
{
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"intron_variant"
],
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"gene_symbol": "PDCD10",
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"transcript": "XM_047447375.1",
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}
],
"gene_symbol": "PDCD10",
"gene_hgnc_id": 8761,
"dbsnp": "rs773691623",
"frequency_reference_population": 0.00033476428,
"hom_count_reference_population": 0,
"allele_count_reference_population": 51,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.000334764,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 51,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9399999976158142,
"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": -0.94,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.338,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000392750.7",
"gene_symbol": "PDCD10",
"hgnc_id": 8761,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
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}
],
"clinvar_disease": "Cerebral cavernous malformation 3",
"clinvar_classification": "not provided",
"clinvar_review_status": "no classification provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Cerebral cavernous malformation 3",
"pathogenicity_classification_combined": "not provided",
"custom_annotations": null
}
],
"message": null
}