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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: 1-17070122-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=17070122&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 17070122,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_007365.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1730A>G",
"hgvs_p": "p.Glu577Gly",
"transcript": "NM_007365.3",
"protein_id": "NP_031391.2",
"transcript_support_level": null,
"aa_start": 577,
"aa_end": null,
"aa_length": 665,
"cds_start": 1730,
"cds_end": null,
"cds_length": 1998,
"cdna_start": 1810,
"cdna_end": null,
"cdna_length": 4361,
"mane_select": "ENST00000375486.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007365.3"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1730A>G",
"hgvs_p": "p.Glu577Gly",
"transcript": "ENST00000375486.9",
"protein_id": "ENSP00000364635.4",
"transcript_support_level": 1,
"aa_start": 577,
"aa_end": null,
"aa_length": 665,
"cds_start": 1730,
"cds_end": null,
"cds_length": 1998,
"cdna_start": 1810,
"cdna_end": null,
"cdna_length": 4361,
"mane_select": "NM_007365.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375486.9"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1796A>G",
"hgvs_p": "p.Glu599Gly",
"transcript": "ENST00000908716.1",
"protein_id": "ENSP00000578775.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 687,
"cds_start": 1796,
"cds_end": null,
"cds_length": 2064,
"cdna_start": 1884,
"cdna_end": null,
"cdna_length": 4435,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908716.1"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1778A>G",
"hgvs_p": "p.Glu593Gly",
"transcript": "ENST00000945841.1",
"protein_id": "ENSP00000615900.1",
"transcript_support_level": null,
"aa_start": 593,
"aa_end": null,
"aa_length": 681,
"cds_start": 1778,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 1860,
"cdna_end": null,
"cdna_length": 3339,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945841.1"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1619A>G",
"hgvs_p": "p.Glu540Gly",
"transcript": "ENST00000908719.1",
"protein_id": "ENSP00000578778.1",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 628,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1887,
"cdna_start": 1699,
"cdna_end": null,
"cdna_length": 4248,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908719.1"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1604A>G",
"hgvs_p": "p.Glu535Gly",
"transcript": "ENST00000908715.1",
"protein_id": "ENSP00000578774.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 623,
"cds_start": 1604,
"cds_end": null,
"cds_length": 1872,
"cdna_start": 1692,
"cdna_end": null,
"cdna_length": 4243,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908715.1"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1424A>G",
"hgvs_p": "p.Glu475Gly",
"transcript": "ENST00000922909.1",
"protein_id": "ENSP00000592968.1",
"transcript_support_level": null,
"aa_start": 475,
"aa_end": null,
"aa_length": 563,
"cds_start": 1424,
"cds_end": null,
"cds_length": 1692,
"cdna_start": 1502,
"cdna_end": null,
"cdna_length": 4052,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922909.1"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1382A>G",
"hgvs_p": "p.Glu461Gly",
"transcript": "ENST00000908717.1",
"protein_id": "ENSP00000578776.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 549,
"cds_start": 1382,
"cds_end": null,
"cds_length": 1650,
"cdna_start": 1462,
"cdna_end": null,
"cdna_length": 4013,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908717.1"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.1229A>G",
"hgvs_p": "p.Glu410Gly",
"transcript": "ENST00000908718.1",
"protein_id": "ENSP00000578777.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 498,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 1309,
"cdna_end": null,
"cdna_length": 3860,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908718.1"
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "c.785A>G",
"hgvs_p": "p.Glu262Gly",
"transcript": "XM_017000148.3",
"protein_id": "XP_016855637.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 350,
"cds_start": 785,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 983,
"cdna_end": null,
"cdna_length": 3534,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000148.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "n.2086A>G",
"hgvs_p": null,
"transcript": "ENST00000466151.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3612,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000466151.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"hgvs_c": "n.677A>G",
"hgvs_p": null,
"transcript": "ENST00000479534.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2389,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000479534.5"
}
],
"gene_symbol": "PADI2",
"gene_hgnc_id": 18341,
"dbsnp": "rs763691887",
"frequency_reference_population": 0.00001982561,
"hom_count_reference_population": 1,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000205224,
"gnomad_genomes_af": 0.0000131354,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06498700380325317,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.07,
"revel_prediction": "Benign",
"alphamissense_score": 0.0774,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.666,
"phylop100way_prediction": "Uncertain_significance",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_007365.3",
"gene_symbol": "PADI2",
"hgnc_id": 18341,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1730A>G",
"hgvs_p": "p.Glu577Gly"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}