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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: 10-22541861-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=22541861&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 22541861,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005028.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.979C>A",
"hgvs_p": "p.Leu327Met",
"transcript": "NM_005028.5",
"protein_id": "NP_005019.2",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 406,
"cds_start": 979,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 1231,
"cdna_end": null,
"cdna_length": 3820,
"mane_select": "ENST00000376573.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.979C>A",
"hgvs_p": "p.Leu327Met",
"transcript": "ENST00000376573.9",
"protein_id": "ENSP00000365757.4",
"transcript_support_level": 1,
"aa_start": 327,
"aa_end": null,
"aa_length": 406,
"cds_start": 979,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 1231,
"cdna_end": null,
"cdna_length": 3820,
"mane_select": "NM_005028.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.802C>A",
"hgvs_p": "p.Leu268Met",
"transcript": "NM_001330062.2",
"protein_id": "NP_001316991.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 347,
"cds_start": 802,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 1008,
"cdna_end": null,
"cdna_length": 3597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.802C>A",
"hgvs_p": "p.Leu268Met",
"transcript": "ENST00000545335.5",
"protein_id": "ENSP00000442098.1",
"transcript_support_level": 2,
"aa_start": 268,
"aa_end": null,
"aa_length": 347,
"cds_start": 802,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 1008,
"cdna_end": null,
"cdna_length": 1436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.559C>A",
"hgvs_p": "p.Leu187Met",
"transcript": "ENST00000323883.11",
"protein_id": "ENSP00000326294.7",
"transcript_support_level": 2,
"aa_start": 187,
"aa_end": null,
"aa_length": 266,
"cds_start": 559,
"cds_end": null,
"cds_length": 801,
"cdna_start": 614,
"cdna_end": null,
"cdna_length": 1319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.826C>A",
"hgvs_p": "p.Leu276Met",
"transcript": "XM_006717450.3",
"protein_id": "XP_006717513.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 355,
"cds_start": 826,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 1078,
"cdna_end": null,
"cdna_length": 3667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.802C>A",
"hgvs_p": "p.Leu268Met",
"transcript": "XM_017016330.2",
"protein_id": "XP_016871819.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 347,
"cds_start": 802,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 978,
"cdna_end": null,
"cdna_length": 3567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.802C>A",
"hgvs_p": "p.Leu268Met",
"transcript": "XM_017016331.2",
"protein_id": "XP_016871820.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 347,
"cds_start": 802,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 6199,
"cdna_end": null,
"cdna_length": 8788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.802C>A",
"hgvs_p": "p.Leu268Met",
"transcript": "XM_047425351.1",
"protein_id": "XP_047281307.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 347,
"cds_start": 802,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 16301,
"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": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"hgvs_c": "c.*91C>A",
"hgvs_p": null,
"transcript": "ENST00000604912.1",
"protein_id": "ENSP00000473858.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 141,
"cds_start": -4,
"cds_end": null,
"cds_length": 426,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PIP4K2A",
"gene_hgnc_id": 8997,
"dbsnp": "rs2230470",
"frequency_reference_population": 0.0010480769,
"hom_count_reference_population": 19,
"allele_count_reference_population": 1681,
"gnomad_exomes_af": 0.000563529,
"gnomad_genomes_af": 0.00566563,
"gnomad_exomes_ac": 818,
"gnomad_genomes_ac": 863,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_homalt": 13,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006621032953262329,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.166,
"revel_prediction": "Benign",
"alphamissense_score": 0.1074,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.753,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005028.5",
"gene_symbol": "PIP4K2A",
"hgnc_id": 8997,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.979C>A",
"hgvs_p": "p.Leu327Met"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}