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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: 3-147396072-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=147396072&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 147396072,
"ref": "C",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001168378.1",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.468G>C",
"hgvs_p": "p.Thr156Thr",
"transcript": "NM_032153.6",
"protein_id": "NP_115529.2",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 334,
"cds_start": 468,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000383075.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032153.6"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.468G>C",
"hgvs_p": "p.Thr156Thr",
"transcript": "ENST00000383075.8",
"protein_id": "ENSP00000372553.3",
"transcript_support_level": 1,
"aa_start": 156,
"aa_end": null,
"aa_length": 334,
"cds_start": 468,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032153.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000383075.8"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.468G>C",
"hgvs_p": "p.Thr156Thr",
"transcript": "ENST00000462748.6",
"protein_id": "ENSP00000420627.2",
"transcript_support_level": 1,
"aa_start": 156,
"aa_end": null,
"aa_length": 228,
"cds_start": 468,
"cds_end": null,
"cds_length": 688,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000462748.6"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.618G>C",
"hgvs_p": "p.Thr206Thr",
"transcript": "NM_001168378.1",
"protein_id": "NP_001161850.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 384,
"cds_start": 618,
"cds_end": null,
"cds_length": 1155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001168378.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.618G>C",
"hgvs_p": "p.Thr206Thr",
"transcript": "ENST00000525172.6",
"protein_id": "ENSP00000435509.2",
"transcript_support_level": 2,
"aa_start": 206,
"aa_end": null,
"aa_length": 384,
"cds_start": 618,
"cds_end": null,
"cds_length": 1155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000525172.6"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.582G>C",
"hgvs_p": "p.Thr194Thr",
"transcript": "NM_001168379.2",
"protein_id": "NP_001161851.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 372,
"cds_start": 582,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001168379.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.582G>C",
"hgvs_p": "p.Thr194Thr",
"transcript": "ENST00000425731.7",
"protein_id": "ENSP00000397695.3",
"transcript_support_level": 2,
"aa_start": 194,
"aa_end": null,
"aa_length": 372,
"cds_start": 582,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000425731.7"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.468G>C",
"hgvs_p": "p.Thr156Thr",
"transcript": "ENST00000473123.5",
"protein_id": "ENSP00000420775.1",
"transcript_support_level": 2,
"aa_start": 156,
"aa_end": null,
"aa_length": 334,
"cds_start": 468,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000473123.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.468G>C",
"hgvs_p": "p.Thr156Thr",
"transcript": "ENST00000484399.5",
"protein_id": "ENSP00000417855.1",
"transcript_support_level": 2,
"aa_start": 156,
"aa_end": null,
"aa_length": 334,
"cds_start": 468,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000484399.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.618G>C",
"hgvs_p": "p.Thr206Thr",
"transcript": "XM_017007314.3",
"protein_id": "XP_016862803.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 291,
"cds_start": 618,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007314.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ZIC1",
"gene_hgnc_id": 12872,
"hgvs_c": "c.46+2130C>G",
"hgvs_p": null,
"transcript": "ENST00000488404.5",
"protein_id": "ENSP00000419664.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 135,
"cds_start": null,
"cds_end": null,
"cds_length": 408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000488404.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.71-4826G>C",
"hgvs_p": null,
"transcript": "NM_001243256.2",
"protein_id": "NP_001230185.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 128,
"cds_start": null,
"cds_end": null,
"cds_length": 387,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001243256.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.71-4826G>C",
"hgvs_p": null,
"transcript": "ENST00000491672.5",
"protein_id": "ENSP00000418277.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 128,
"cds_start": null,
"cds_end": null,
"cds_length": 387,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000491672.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "n.1115G>C",
"hgvs_p": null,
"transcript": "ENST00000493664.5",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000493664.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ZIC1",
"gene_hgnc_id": 12872,
"hgvs_c": "n.521+2130C>G",
"hgvs_p": null,
"transcript": "ENST00000472523.1",
"protein_id": null,
"transcript_support_level": 4,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000472523.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"hgvs_c": "c.*235G>C",
"hgvs_p": null,
"transcript": "ENST00000484586.5",
"protein_id": "ENSP00000418343.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 76,
"cds_start": null,
"cds_end": null,
"cds_length": 233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000484586.5"
}
],
"gene_symbol": "ZIC4",
"gene_hgnc_id": 20393,
"dbsnp": "rs376509983",
"frequency_reference_population": 0.0000020521577,
"hom_count_reference_population": 1,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205216,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.108,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP7",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_001168378.1",
"gene_symbol": "ZIC4",
"hgnc_id": 20393,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.618G>C",
"hgvs_p": "p.Thr206Thr"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000472523.1",
"gene_symbol": "ZIC1",
"hgnc_id": 12872,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "n.521+2130C>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}