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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: 13-19719577-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=19719577&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 19719577,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000338910.9",
"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": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "c.1159-9978G>A",
"hgvs_p": null,
"transcript": "NM_001354909.2",
"protein_id": "NP_001341838.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 523,
"cds_start": -4,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2435,
"mane_select": "ENST00000338910.9",
"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": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "c.1159-9978G>A",
"hgvs_p": null,
"transcript": "ENST00000338910.9",
"protein_id": "ENSP00000343966.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 523,
"cds_start": -4,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2435,
"mane_select": "NM_001354909.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1158+10662G>A",
"hgvs_p": null,
"transcript": "ENST00000471658.5",
"protein_id": "ENSP00000436038.1",
"transcript_support_level": 1,
"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": 1647,
"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": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "c.1159-9978G>A",
"hgvs_p": null,
"transcript": "NM_001042414.4",
"protein_id": "NP_001035879.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 523,
"cds_start": -4,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2310,
"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": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "c.1159-9978G>A",
"hgvs_p": null,
"transcript": "ENST00000619300.4",
"protein_id": "ENSP00000481916.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 523,
"cds_start": -4,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2013,
"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": 7,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "c.1187+1876G>A",
"hgvs_p": null,
"transcript": "NM_001354908.2",
"protein_id": "NP_001341837.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 417,
"cds_start": -4,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1708,
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "c.1158+10662G>A",
"hgvs_p": null,
"transcript": "NM_001363660.2",
"protein_id": "NP_001350589.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1158+10662G>A",
"hgvs_p": null,
"transcript": "ENST00000492741.5",
"protein_id": "ENSP00000435921.1",
"transcript_support_level": 2,
"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": 1709,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.78+10662G>A",
"hgvs_p": null,
"transcript": "ENST00000635562.1",
"protein_id": "ENSP00000488975.1",
"transcript_support_level": 3,
"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": 422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1346+10662G>A",
"hgvs_p": null,
"transcript": "NR_003272.4",
"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": 1679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1346+10662G>A",
"hgvs_p": null,
"transcript": "NR_044998.3",
"protein_id": null,
"transcript_support_level": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 10,
"intron_rank": 6,
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"gene_symbol": "PSPC1",
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"hgvs_c": "n.1347-9978G>A",
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"transcript": "NR_149052.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"biotype": null,
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 6,
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"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1346+10662G>A",
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"transcript": "NR_149053.2",
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1346+10662G>A",
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"transcript": "NR_156729.2",
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},
{
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"strand": false,
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"intron_variant"
],
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"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "c.1158+10662G>A",
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"transcript": "XM_011535138.4",
"protein_id": "XP_011533440.1",
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"mane_select": null,
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"biotype": null,
"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": 7,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "c.1187+1876G>A",
"hgvs_p": null,
"transcript": "XM_011535139.3",
"protein_id": "XP_011533441.1",
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},
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],
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"gene_symbol": "PSPC1",
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"hgvs_c": "c.1187+1876G>A",
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"transcript": "XM_047430435.1",
"protein_id": "XP_047286391.1",
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 10,
"intron_rank": 6,
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"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1347-9978G>A",
"hgvs_p": null,
"transcript": "XR_007063688.1",
"protein_id": null,
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1346+10662G>A",
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"transcript": "XR_007063689.1",
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 10,
"intron_rank": 6,
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"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"hgvs_c": "n.1347-9978G>A",
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"transcript": "XR_941617.3",
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}
],
"gene_symbol": "PSPC1",
"gene_hgnc_id": 20320,
"dbsnp": "rs9551988",
"frequency_reference_population": 0.11950694,
"hom_count_reference_population": 1218,
"allele_count_reference_population": 18188,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.119507,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 18188,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 1218,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8899999856948853,
"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": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.787,
"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": "ENST00000338910.9",
"gene_symbol": "PSPC1",
"hgnc_id": 20320,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1159-9978G>A",
"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
}