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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: 2-97734655-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=97734655&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 97734655,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001079.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "NM_001079.4",
"protein_id": "NP_001070.2",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 619,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1224,
"cdna_end": null,
"cdna_length": 2421,
"mane_select": "ENST00000264972.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001079.4"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000264972.10",
"protein_id": "ENSP00000264972.5",
"transcript_support_level": 1,
"aa_start": 342,
"aa_end": null,
"aa_length": 619,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1224,
"cdna_end": null,
"cdna_length": 2421,
"mane_select": "NM_001079.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264972.10"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.104T>C",
"hgvs_p": "p.Ile35Thr",
"transcript": "ENST00000451498.2",
"protein_id": "ENSP00000400475.2",
"transcript_support_level": 1,
"aa_start": 35,
"aa_end": null,
"aa_length": 312,
"cds_start": 104,
"cds_end": null,
"cds_length": 939,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 1085,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000451498.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.886T>C",
"hgvs_p": null,
"transcript": "ENST00000463643.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2085,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000463643.5"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "NM_001378594.1",
"protein_id": "NP_001365523.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 619,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1159,
"cdna_end": null,
"cdna_length": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001378594.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000698508.2",
"protein_id": "ENSP00000513759.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 619,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1225,
"cdna_end": null,
"cdna_length": 3088,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000698508.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000885386.1",
"protein_id": "ENSP00000555445.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 619,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1212,
"cdna_end": null,
"cdna_length": 2407,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885386.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000885387.1",
"protein_id": "ENSP00000555446.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 619,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2338,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885387.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.896T>C",
"hgvs_p": "p.Ile299Thr",
"transcript": "ENST00000885385.1",
"protein_id": "ENSP00000555444.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 576,
"cds_start": 896,
"cds_end": null,
"cds_length": 1731,
"cdna_start": 1095,
"cdna_end": null,
"cdna_length": 2292,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885385.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.104T>C",
"hgvs_p": "p.Ile35Thr",
"transcript": "NM_207519.2",
"protein_id": "NP_997402.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 312,
"cds_start": 104,
"cds_end": null,
"cds_length": 939,
"cdna_start": 1356,
"cdna_end": null,
"cdna_length": 2553,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_207519.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1007T>C",
"hgvs_p": "p.Ile336Thr",
"transcript": "XM_047445774.1",
"protein_id": "XP_047301730.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 613,
"cds_start": 1007,
"cds_end": null,
"cds_length": 1842,
"cdna_start": 1206,
"cdna_end": null,
"cdna_length": 2403,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445774.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "XM_047445775.1",
"protein_id": "XP_047301731.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 607,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1824,
"cdna_start": 1224,
"cdna_end": null,
"cdna_length": 16978,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445775.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "c.1007T>C",
"hgvs_p": "p.Ile336Thr",
"transcript": "XM_047445776.1",
"protein_id": "XP_047301732.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 601,
"cds_start": 1007,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 1206,
"cdna_end": null,
"cdna_length": 16960,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445776.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.1540T>C",
"hgvs_p": null,
"transcript": "ENST00000487283.5",
"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": 3273,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000487283.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.1165T>C",
"hgvs_p": null,
"transcript": "ENST00000698509.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2112,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000698509.1"
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.*141T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4935,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000718250.1"
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.1224T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 15411,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007081582.1"
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.1224T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2630,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007081583.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"hgvs_c": "n.*141T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4935,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000718250.1"
}
],
"gene_symbol": "ZAP70",
"gene_hgnc_id": 12858,
"dbsnp": "rs142702703",
"frequency_reference_population": 0.0005036569,
"hom_count_reference_population": 0,
"allele_count_reference_population": 813,
"gnomad_exomes_af": 0.00049116,
"gnomad_genomes_af": 0.000623564,
"gnomad_exomes_ac": 718,
"gnomad_genomes_ac": 95,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009921610355377197,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.297,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1261,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.425,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_001079.4",
"gene_symbol": "ZAP70",
"hgnc_id": 12858,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr"
}
],
"clinvar_disease": "Combined immunodeficiency due to ZAP70 deficiency,ZAP70-Related Severe Combined Immunodeficiency,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:2",
"phenotype_combined": "Combined immunodeficiency due to ZAP70 deficiency|ZAP70-Related Severe Combined Immunodeficiency|not provided|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}