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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: 17-38778345-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=38778345&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PIP4K2B",
"hgnc_id": 8998,
"hgvs_c": "c.682G>A",
"hgvs_p": "p.Asp228Asn",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_003559.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 22,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.6189,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"chr": "17",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.20231080055236816,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 416,
"aa_ref": "D",
"aa_start": 228,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5383,
"cdna_start": 814,
"cds_end": null,
"cds_length": 1251,
"cds_start": 682,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_003559.5",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.682G>A",
"hgvs_p": "p.Asp228Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000619039.5",
"protein_coding": true,
"protein_id": "NP_003550.1",
"strand": false,
"transcript": "NM_003559.5",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 416,
"aa_ref": "D",
"aa_start": 228,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5383,
"cdna_start": 814,
"cds_end": null,
"cds_length": 1251,
"cds_start": 682,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000619039.5",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.682G>A",
"hgvs_p": "p.Asp228Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003559.5",
"protein_coding": true,
"protein_id": "ENSP00000482548.1",
"strand": false,
"transcript": "ENST00000619039.5",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 367,
"aa_ref": "D",
"aa_start": 228,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5196,
"cdna_start": 776,
"cds_end": null,
"cds_length": 1104,
"cds_start": 682,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000862415.1",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.682G>A",
"hgvs_p": "p.Asp228Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532474.1",
"strand": false,
"transcript": "ENST00000862415.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 443,
"aa_ref": "D",
"aa_start": 255,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5464,
"cdna_start": 895,
"cds_end": null,
"cds_length": 1332,
"cds_start": 763,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011525326.4",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.763G>A",
"hgvs_p": "p.Asp255Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523628.1",
"strand": false,
"transcript": "XM_011525326.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 379,
"aa_ref": "D",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5595,
"cdna_start": 1026,
"cds_end": null,
"cds_length": 1140,
"cds_start": 571,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_011525327.3",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Asp191Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523629.1",
"strand": false,
"transcript": "XM_011525327.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 379,
"aa_ref": "D",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5624,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 1140,
"cds_start": 571,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047436888.1",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Asp191Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292844.1",
"strand": false,
"transcript": "XM_047436888.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 352,
"aa_ref": "D",
"aa_start": 164,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5543,
"cdna_start": 974,
"cds_end": null,
"cds_length": 1059,
"cds_start": 490,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047436889.1",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.490G>A",
"hgvs_p": "p.Asp164Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292845.1",
"strand": false,
"transcript": "XM_047436889.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 284,
"aa_ref": "D",
"aa_start": 96,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5068,
"cdna_start": 499,
"cds_end": null,
"cds_length": 855,
"cds_start": 286,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011525330.2",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.286G>A",
"hgvs_p": "p.Asp96Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523632.1",
"strand": false,
"transcript": "XM_011525330.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 248,
"aa_ref": "D",
"aa_start": 60,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4992,
"cdna_start": 423,
"cds_end": null,
"cds_length": 747,
"cds_start": 178,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047436890.1",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "c.178G>A",
"hgvs_p": "p.Asp60Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292846.1",
"strand": false,
"transcript": "XM_047436890.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 478,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000613767.4",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "n.254G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000613767.4",
"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": 927,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000617781.1",
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"hgvs_c": "n.780G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000617781.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs762235703",
"effect": "missense_variant",
"frequency_reference_population": 0.000013630072,
"gene_hgnc_id": 8998,
"gene_symbol": "PIP4K2B",
"gnomad_exomes_ac": 18,
"gnomad_exomes_af": 0.0000123134,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262726,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.557,
"pos": 38778345,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.127,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003559.5"
}
]
}