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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: 9-129125837-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=129125837&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 129125837,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000393370.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.216+2699A>G",
"hgvs_p": null,
"transcript": "NM_178000.3",
"protein_id": "NP_821067.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 323,
"cds_start": -4,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2640,
"mane_select": "ENST00000393370.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.216+2699A>G",
"hgvs_p": null,
"transcript": "ENST00000393370.7",
"protein_id": "ENSP00000377036.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 323,
"cds_start": -4,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2640,
"mane_select": "NM_178000.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.366+2699A>G",
"hgvs_p": null,
"transcript": "ENST00000358994.9",
"protein_id": "ENSP00000351885.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 373,
"cds_start": -4,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.111+2699A>G",
"hgvs_p": null,
"transcript": "ENST00000452489.6",
"protein_id": "ENSP00000394338.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": -4,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.129+5227A>G",
"hgvs_p": null,
"transcript": "ENST00000347048.8",
"protein_id": "ENSP00000337412.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 104,
"cds_start": -4,
"cds_end": null,
"cds_length": 315,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.217-2127A>G",
"hgvs_p": null,
"transcript": "NM_178001.3",
"protein_id": "NP_821068.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 358,
"cds_start": -4,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.217-2127A>G",
"hgvs_p": null,
"transcript": "ENST00000337738.6",
"protein_id": "ENSP00000337448.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 358,
"cds_start": -4,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.234+2699A>G",
"hgvs_p": null,
"transcript": "ENST00000348141.9",
"protein_id": "ENSP00000335200.6",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 329,
"cds_start": -4,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.216+2699A>G",
"hgvs_p": null,
"transcript": "NM_021131.5",
"protein_id": "NP_066954.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 323,
"cds_start": -4,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.367-2127A>G",
"hgvs_p": null,
"transcript": "ENST00000455292.6",
"protein_id": "ENSP00000395499.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 901,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.130-3148A>G",
"hgvs_p": null,
"transcript": "NM_001271832.2",
"protein_id": "NP_001258761.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 294,
"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 9,
"intron_rank": 2,
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"gene_symbol": "PTPA",
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"hgvs_c": "c.130-3148A>G",
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"transcript": "ENST00000357197.8",
"protein_id": "ENSP00000349726.4",
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},
{
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"strand": true,
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"intron_variant"
],
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"exon_count": 10,
"intron_rank": 3,
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"gene_symbol": "PTPA",
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"hgvs_c": "c.111+2699A>G",
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"transcript": "NM_001193397.2",
"protein_id": "NP_001180326.1",
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 9,
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"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.216+2699A>G",
"hgvs_p": null,
"transcript": "NM_178003.3",
"protein_id": "NP_821070.1",
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},
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],
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"gene_symbol": "PTPA",
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"hgvs_c": "c.216+2699A>G",
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"transcript": "ENST00000355007.7",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPA",
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"hgvs_c": "c.285+2699A>G",
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"transcript": "ENST00000417504.5",
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},
{
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],
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"gene_symbol": "PTPA",
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"hgvs_c": "c.1-2127A>G",
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"transcript": "ENST00000414331.5",
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},
{
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],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 3,
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"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.111+2699A>G",
"hgvs_p": null,
"transcript": "ENST00000453358.5",
"protein_id": "ENSP00000393092.1",
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},
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"consequences": [
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],
"exon_rank": null,
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"exon_count": 4,
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"gene_symbol": "PTPA",
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"hgvs_c": "c.111+2699A>G",
"hgvs_p": null,
"transcript": "ENST00000440346.1",
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},
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],
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},
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],
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},
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTPA",
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"hgvs_c": "c.280-3148A>G",
"hgvs_p": null,
"transcript": "XM_011518836.3",
"protein_id": "XP_011517138.1",
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTPA",
"gene_hgnc_id": 9308,
"hgvs_c": "c.367-2127A>G",
"hgvs_p": null,
"transcript": "XM_047423560.1",
"protein_id": "XP_047279516.1",
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},
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"gene_symbol": "PTPA",
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"transcript": "XM_011518838.3",
"protein_id": "XP_011517140.1",
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"cds_start": -4,
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}
],
"gene_symbol": "PTPA",
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"dbsnp": "rs10988217",
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"hom_count_reference_population": 18858,
"allele_count_reference_population": 68727,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.451747,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 68727,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 18858,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"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": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.592,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000393370.7",
"gene_symbol": "PTPA",
"hgnc_id": 9308,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.216+2699A>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}