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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: 16-25240424-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=25240424&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ZKSCAN2",
"hgnc_id": 25677,
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Trp",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_001012981.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 32,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.2299,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.23,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5605984330177307,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 967,
"aa_ref": "R",
"aa_start": 766,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7437,
"cdna_start": 3014,
"cds_end": null,
"cds_length": 2904,
"cds_start": 2296,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001012981.5",
"gene_hgnc_id": 25677,
"gene_symbol": "ZKSCAN2",
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000328086.12",
"protein_coding": true,
"protein_id": "NP_001012999.3",
"strand": false,
"transcript": "NM_001012981.5",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 967,
"aa_ref": "R",
"aa_start": 766,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7437,
"cdna_start": 3014,
"cds_end": null,
"cds_length": 2904,
"cds_start": 2296,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000328086.12",
"gene_hgnc_id": 25677,
"gene_symbol": "ZKSCAN2",
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001012981.5",
"protein_coding": true,
"protein_id": "ENSP00000331626.7",
"strand": false,
"transcript": "ENST00000328086.12",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 803,
"aa_ref": "R",
"aa_start": 602,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6897,
"cdna_start": 2495,
"cds_end": null,
"cds_length": 2412,
"cds_start": 1804,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000919970.1",
"gene_hgnc_id": 25677,
"gene_symbol": "ZKSCAN2",
"hgvs_c": "c.1804C>T",
"hgvs_p": "p.Arg602Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590029.1",
"strand": false,
"transcript": "ENST00000919970.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 575,
"aa_ref": "R",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6213,
"cdna_start": 1816,
"cds_end": null,
"cds_length": 1728,
"cds_start": 1120,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000964638.1",
"gene_hgnc_id": 25677,
"gene_symbol": "ZKSCAN2",
"hgvs_c": "c.1120C>T",
"hgvs_p": "p.Arg374Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634697.1",
"strand": false,
"transcript": "ENST00000964638.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 763,
"aa_ref": "R",
"aa_start": 562,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6246,
"cdna_start": 1823,
"cds_end": null,
"cds_length": 2292,
"cds_start": 1684,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_017023200.3",
"gene_hgnc_id": 25677,
"gene_symbol": "ZKSCAN2",
"hgvs_c": "c.1684C>T",
"hgvs_p": "p.Arg562Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016878689.1",
"strand": false,
"transcript": "XM_017023200.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3667,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000569150.1",
"gene_hgnc_id": 25677,
"gene_symbol": "ZKSCAN2",
"hgvs_c": "n.*1608C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455586.1",
"strand": false,
"transcript": "ENST00000569150.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3667,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000569150.1",
"gene_hgnc_id": 25677,
"gene_symbol": "ZKSCAN2",
"hgvs_c": "n.*1608C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455586.1",
"strand": false,
"transcript": "ENST00000569150.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs752800344",
"effect": "missense_variant",
"frequency_reference_population": 0.00001982701,
"gene_hgnc_id": 25677,
"gene_symbol": "ZKSCAN2",
"gnomad_exomes_ac": 29,
"gnomad_exomes_af": 0.0000198377,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197239,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.189,
"pos": 25240424,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.232,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001012981.5"
}
]
}