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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: 10-22573355-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=22573355&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 22573355,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000376573.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.595G>A",
"hgvs_p": "p.Val199Ile",
"transcript": "NM_005028.5",
"protein_id": "NP_005019.2",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 406,
"cds_start": 595,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 847,
"cdna_end": null,
"cdna_length": 3820,
"mane_select": "ENST00000376573.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.595G>A",
"hgvs_p": "p.Val199Ile",
"transcript": "ENST00000376573.9",
"protein_id": "ENSP00000365757.4",
"transcript_support_level": 1,
"aa_start": 199,
"aa_end": null,
"aa_length": 406,
"cds_start": 595,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 847,
"cdna_end": null,
"cdna_length": 3820,
"mane_select": "NM_005028.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.418G>A",
"hgvs_p": "p.Val140Ile",
"transcript": "NM_001330062.2",
"protein_id": "NP_001316991.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 347,
"cds_start": 418,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 624,
"cdna_end": null,
"cdna_length": 3597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.418G>A",
"hgvs_p": "p.Val140Ile",
"transcript": "ENST00000545335.5",
"protein_id": "ENSP00000442098.1",
"transcript_support_level": 2,
"aa_start": 140,
"aa_end": null,
"aa_length": 347,
"cds_start": 418,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 624,
"cdna_end": null,
"cdna_length": 1436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.133G>A",
"hgvs_p": "p.Val45Ile",
"transcript": "ENST00000323883.11",
"protein_id": "ENSP00000326294.7",
"transcript_support_level": 2,
"aa_start": 45,
"aa_end": null,
"aa_length": 266,
"cds_start": 133,
"cds_end": null,
"cds_length": 801,
"cdna_start": 188,
"cdna_end": null,
"cdna_length": 1319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.133G>A",
"hgvs_p": "p.Val45Ile",
"transcript": "ENST00000604912.1",
"protein_id": "ENSP00000473858.1",
"transcript_support_level": 2,
"aa_start": 45,
"aa_end": null,
"aa_length": 141,
"cds_start": 133,
"cds_end": null,
"cds_length": 426,
"cdna_start": 150,
"cdna_end": null,
"cdna_length": 443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.442G>A",
"hgvs_p": "p.Val148Ile",
"transcript": "XM_006717450.3",
"protein_id": "XP_006717513.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 355,
"cds_start": 442,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 694,
"cdna_end": null,
"cdna_length": 3667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.418G>A",
"hgvs_p": "p.Val140Ile",
"transcript": "XM_017016330.2",
"protein_id": "XP_016871819.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 347,
"cds_start": 418,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 594,
"cdna_end": null,
"cdna_length": 3567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.418G>A",
"hgvs_p": "p.Val140Ile",
"transcript": "XM_017016331.2",
"protein_id": "XP_016871820.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 347,
"cds_start": 418,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 5815,
"cdna_end": null,
"cdna_length": 8788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.418G>A",
"hgvs_p": "p.Val140Ile",
"transcript": "XM_047425351.1",
"protein_id": "XP_047281307.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 347,
"cds_start": 418,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 15917,
"cdna_end": null,
"cdna_length": 18890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "n.451G>A",
"hgvs_p": null,
"transcript": "ENST00000422321.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"dbsnp": null,
"frequency_reference_population": 6.842894e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84289e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5166151523590088,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.132,
"revel_prediction": "Benign",
"alphamissense_score": 0.1232,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.532,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000376573.9",
"gene_symbol": "PIP4K2A",
"hgnc_id": 8997,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.595G>A",
"hgvs_p": "p.Val199Ile"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}