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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: 10-103409718-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=103409718&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PDCD11",
"hgnc_id": 13408,
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001411058.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 32,
"alphamissense_prediction": null,
"alphamissense_score": 0.0766,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.61,
"chr": "10",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.1046271026134491,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1871,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6477,
"cdna_start": 1006,
"cds_end": null,
"cds_length": 5616,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_014976.2",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000369797.8",
"protein_coding": true,
"protein_id": "NP_055791.1",
"strand": true,
"transcript": "NM_014976.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1871,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6477,
"cdna_start": 1006,
"cds_end": null,
"cds_length": 5616,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000369797.8",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014976.2",
"protein_coding": true,
"protein_id": "ENSP00000358812.3",
"strand": true,
"transcript": "ENST00000369797.8",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1897,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6507,
"cdna_start": 958,
"cds_end": null,
"cds_length": 5694,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930114.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600173.1",
"strand": true,
"transcript": "ENST00000930114.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1872,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6445,
"cdna_start": 971,
"cds_end": null,
"cds_length": 5619,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001411058.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397987.1",
"strand": true,
"transcript": "NM_001411058.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1872,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6480,
"cdna_start": 1006,
"cds_end": null,
"cds_length": 5619,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001437421.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001424350.1",
"strand": true,
"transcript": "NM_001437421.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1872,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6467,
"cdna_start": 1006,
"cds_end": null,
"cds_length": 5619,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000649849.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000498205.1",
"strand": true,
"transcript": "ENST00000649849.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1872,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6448,
"cdna_start": 971,
"cds_end": null,
"cds_length": 5619,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930107.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600166.1",
"strand": true,
"transcript": "ENST00000930107.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1872,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6408,
"cdna_start": 934,
"cds_end": null,
"cds_length": 5619,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930117.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600176.1",
"strand": true,
"transcript": "ENST00000930117.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1871,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6442,
"cdna_start": 971,
"cds_end": null,
"cds_length": 5616,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001437420.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001424349.1",
"strand": true,
"transcript": "NM_001437420.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1871,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6441,
"cdna_start": 971,
"cds_end": null,
"cds_length": 5616,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930108.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600167.1",
"strand": true,
"transcript": "ENST00000930108.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1871,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6533,
"cdna_start": 1064,
"cds_end": null,
"cds_length": 5616,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000930109.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600168.1",
"strand": true,
"transcript": "ENST00000930109.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1871,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6405,
"cdna_start": 933,
"cds_end": null,
"cds_length": 5616,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930110.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600169.1",
"strand": true,
"transcript": "ENST00000930110.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1871,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6496,
"cdna_start": 1024,
"cds_end": null,
"cds_length": 5616,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000930116.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600175.1",
"strand": true,
"transcript": "ENST00000930116.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1870,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6453,
"cdna_start": 983,
"cds_end": null,
"cds_length": 5613,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930111.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600170.1",
"strand": true,
"transcript": "ENST00000930111.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1850,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6385,
"cdna_start": 977,
"cds_end": null,
"cds_length": 5553,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930112.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600171.1",
"strand": true,
"transcript": "ENST00000930112.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1846,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6350,
"cdna_start": 952,
"cds_end": null,
"cds_length": 5541,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930115.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600174.1",
"strand": true,
"transcript": "ENST00000930115.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1831,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6349,
"cdna_start": 1000,
"cds_end": null,
"cds_length": 5496,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000902786.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572845.1",
"strand": true,
"transcript": "ENST00000902786.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1811,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6257,
"cdna_start": 966,
"cds_end": null,
"cds_length": 5436,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000930113.1",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600172.1",
"strand": true,
"transcript": "ENST00000930113.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1789,
"aa_ref": "T",
"aa_start": 214,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6305,
"cdna_start": 831,
"cds_end": null,
"cds_length": 5370,
"cds_start": 641,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011539540.2",
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"hgvs_c": "c.641C>T",
"hgvs_p": "p.Thr214Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011537842.1",
"strand": true,
"transcript": "XM_011539540.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs772637975",
"effect": "missense_variant",
"frequency_reference_population": 0.00001983094,
"gene_hgnc_id": 13408,
"gene_symbol": "PDCD11",
"gnomad_exomes_ac": 30,
"gnomad_exomes_af": 0.0000205266,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131473,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.179,
"pos": 103409718,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.089,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_001411058.1"
}
]
}