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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: 2-97737576-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=97737576&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 97737576,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000264972.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1393C>T",
"hgvs_p": "p.Arg465Cys",
"transcript": "NM_001079.4",
"protein_id": "NP_001070.2",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 619,
"cds_start": 1393,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1592,
"cdna_end": null,
"cdna_length": 2421,
"mane_select": "ENST00000264972.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1393C>T",
"hgvs_p": "p.Arg465Cys",
"transcript": "ENST00000264972.10",
"protein_id": "ENSP00000264972.5",
"transcript_support_level": 1,
"aa_start": 465,
"aa_end": null,
"aa_length": 619,
"cds_start": 1393,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1592,
"cdna_end": null,
"cdna_length": 2421,
"mane_select": "NM_001079.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "ENST00000451498.2",
"protein_id": "ENSP00000400475.2",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 312,
"cds_start": 472,
"cds_end": null,
"cds_length": 939,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 1085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.1254C>T",
"hgvs_p": null,
"transcript": "ENST00000463643.5",
"protein_id": null,
"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": 2085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1393C>T",
"hgvs_p": "p.Arg465Cys",
"transcript": "NM_001378594.1",
"protein_id": "NP_001365523.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 619,
"cds_start": 1393,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1527,
"cdna_end": null,
"cdna_length": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1393C>T",
"hgvs_p": "p.Arg465Cys",
"transcript": "ENST00000698508.2",
"protein_id": "ENSP00000513759.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 619,
"cds_start": 1393,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1593,
"cdna_end": null,
"cdna_length": 3088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "NM_207519.2",
"protein_id": "NP_997402.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 312,
"cds_start": 472,
"cds_end": null,
"cds_length": 939,
"cdna_start": 1724,
"cdna_end": null,
"cdna_length": 2553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1375C>T",
"hgvs_p": "p.Arg459Cys",
"transcript": "XM_047445774.1",
"protein_id": "XP_047301730.1",
"transcript_support_level": null,
"aa_start": 459,
"aa_end": null,
"aa_length": 613,
"cds_start": 1375,
"cds_end": null,
"cds_length": 1842,
"cdna_start": 1574,
"cdna_end": null,
"cdna_length": 2403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1393C>T",
"hgvs_p": "p.Arg465Cys",
"transcript": "XM_047445775.1",
"protein_id": "XP_047301731.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 607,
"cds_start": 1393,
"cds_end": null,
"cds_length": 1824,
"cdna_start": 1592,
"cdna_end": null,
"cdna_length": 16978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1375C>T",
"hgvs_p": "p.Arg459Cys",
"transcript": "XM_047445776.1",
"protein_id": "XP_047301732.1",
"transcript_support_level": null,
"aa_start": 459,
"aa_end": null,
"aa_length": 601,
"cds_start": 1375,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 1574,
"cdna_end": null,
"cdna_length": 16960,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.2445C>T",
"hgvs_p": null,
"transcript": "ENST00000487283.5",
"protein_id": null,
"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": 3273,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.331C>T",
"hgvs_p": null,
"transcript": "ENST00000495754.1",
"protein_id": null,
"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": 675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.1533C>T",
"hgvs_p": null,
"transcript": "ENST00000698509.1",
"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": 2112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.*509C>T",
"hgvs_p": null,
"transcript": "ENST00000718250.1",
"protein_id": "ENSP00000520695.1",
"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": 4935,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.1592C>T",
"hgvs_p": null,
"transcript": "XR_007081582.1",
"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": 15411,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.1592C>T",
"hgvs_p": null,
"transcript": "XR_007081583.1",
"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": 2630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.*509C>T",
"hgvs_p": null,
"transcript": "ENST00000718250.1",
"protein_id": "ENSP00000520695.1",
"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": 4935,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.-246C>T",
"hgvs_p": null,
"transcript": "ENST00000489250.1",
"protein_id": null,
"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": 659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"dbsnp": "rs113994174",
"frequency_reference_population": 0.000005576222,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000478849,
"gnomad_genomes_af": 0.0000131444,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9943768978118896,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.847,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9988,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.36,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.109,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000264972.10",
"gene_symbol": "ZAP70",
"hgnc_id": 12858,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1393C>T",
"hgvs_p": "p.Arg465Cys"
}
],
"clinvar_disease": " 2, infantile-onset, multisystem,Autoimmune disease,Combined immunodeficiency due to ZAP70 deficiency,Severe combined immunodeficiency disease",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2 O:1",
"phenotype_combined": "Combined immunodeficiency due to ZAP70 deficiency|Severe combined immunodeficiency disease|Combined immunodeficiency due to ZAP70 deficiency;Autoimmune disease, multisystem, infantile-onset, 2",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}