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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: 3-147403964-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=147403964&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 19,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"gene_symbol": "ZIC4",
"hgnc_id": 20393,
"hgvs_c": "c.135G>A",
"hgvs_p": "p.Lys45Lys",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -19,
"transcript": "NM_001168378.1",
"verdict": "Benign"
},
{
"benign_score": 18,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ZIC1",
"hgnc_id": 12872,
"hgvs_c": "n.521+10022C>T",
"hgvs_p": null,
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 0,
"score": -18,
"transcript": "ENST00000472523.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BA1",
"acmg_score": -19,
"allele_count_reference_population": 323084,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"chr": "3",
"clinvar_classification": "Benign",
"clinvar_disease": "not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.1899999976158142,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 334,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4014,
"cdna_start": null,
"cds_end": null,
"cds_length": 1005,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_032153.6",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-15-1152G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000383075.8",
"protein_coding": true,
"protein_id": "NP_115529.2",
"strand": false,
"transcript": "NM_032153.6",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 334,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4014,
"cdna_start": null,
"cds_end": null,
"cds_length": 1005,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000383075.8",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-15-1152G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032153.6",
"protein_coding": true,
"protein_id": "ENSP00000372553.3",
"strand": false,
"transcript": "ENST00000383075.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 228,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 929,
"cdna_start": null,
"cds_end": null,
"cds_length": 688,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000462748.6",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-15-1152G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420627.2",
"strand": false,
"transcript": "ENST00000462748.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 334,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1774,
"cdna_start": null,
"cds_end": null,
"cds_length": 1005,
"cds_start": null,
"consequences": [
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000484399.5",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-16G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417855.1",
"strand": false,
"transcript": "ENST00000484399.5",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 384,
"aa_ref": "K",
"aa_start": 45,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4152,
"cdna_start": 321,
"cds_end": null,
"cds_length": 1155,
"cds_start": 135,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001168378.1",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.135G>A",
"hgvs_p": "p.Lys45Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001161850.1",
"strand": false,
"transcript": "NM_001168378.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 384,
"aa_ref": "K",
"aa_start": 45,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4152,
"cdna_start": 321,
"cds_end": null,
"cds_length": 1155,
"cds_start": 135,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000525172.6",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.135G>A",
"hgvs_p": "p.Lys45Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000435509.2",
"strand": false,
"transcript": "ENST00000525172.6",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 291,
"aa_ref": "K",
"aa_start": 45,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1149,
"cdna_start": 321,
"cds_end": null,
"cds_length": 876,
"cds_start": 135,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_017007314.3",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.135G>A",
"hgvs_p": "p.Lys45Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016862803.1",
"strand": false,
"transcript": "XM_017007314.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 334,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1774,
"cdna_start": null,
"cds_end": null,
"cds_length": 1005,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000484399.5",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-16G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417855.1",
"strand": false,
"transcript": "ENST00000484399.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 372,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3981,
"cdna_start": null,
"cds_end": null,
"cds_length": 1119,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001168379.2",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.100-1152G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001161851.1",
"strand": false,
"transcript": "NM_001168379.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 372,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3979,
"cdna_start": null,
"cds_end": null,
"cds_length": 1119,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000425731.7",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.100-1152G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000397695.3",
"strand": false,
"transcript": "ENST00000425731.7",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 334,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1481,
"cdna_start": null,
"cds_end": null,
"cds_length": 1005,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000473123.5",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-15-1152G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420775.1",
"strand": false,
"transcript": "ENST00000473123.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 135,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 539,
"cdna_start": null,
"cds_end": null,
"cds_length": 408,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000488404.5",
"gene_hgnc_id": 12872,
"gene_symbol": "ZIC1",
"hgvs_c": "c.47-8554C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419664.1",
"strand": true,
"transcript": "ENST00000488404.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 128,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3396,
"cdna_start": null,
"cds_end": null,
"cds_length": 387,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001243256.2",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-15-1152G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001230185.1",
"strand": false,
"transcript": "NM_001243256.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 128,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 925,
"cdna_start": null,
"cds_end": null,
"cds_length": 387,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000491672.5",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-15-1152G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418277.1",
"strand": false,
"transcript": "ENST00000491672.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 67,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 565,
"cdna_start": null,
"cds_end": null,
"cds_length": 205,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000463250.1",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-15-1152G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419727.1",
"strand": false,
"transcript": "ENST00000463250.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 567,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000472523.1",
"gene_hgnc_id": 12872,
"gene_symbol": "ZIC1",
"hgvs_c": "n.521+10022C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000472523.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 76,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 500,
"cdna_start": null,
"cds_end": null,
"cds_length": 233,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000484586.5",
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"hgvs_c": "c.-433G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418343.1",
"strand": true,
"transcript": "ENST00000484586.5",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.658484538100456,
"dbsnp": "rs6766244",
"effect": "splice_region_variant,synonymous_variant",
"frequency_reference_population": 0.21030527,
"gene_hgnc_id": 20393,
"gene_symbol": "ZIC4",
"gnomad_exomes_ac": 295935,
"gnomad_exomes_af": 0.213808,
"gnomad_exomes_homalt": 33219,
"gnomad_genomes_ac": 27149,
"gnomad_genomes_af": 0.178438,
"gnomad_genomes_homalt": 2651,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 35870,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.315,
"pos": 147403964,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.2639999985694885,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001168378.1"
}
]
}