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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: X-18908052-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=18908052&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 18908052,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000379942.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Pro789Ser",
"transcript": "NM_000292.3",
"protein_id": "NP_000283.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 1235,
"cds_start": 2365,
"cds_end": null,
"cds_length": 3708,
"cdna_start": 2547,
"cdna_end": null,
"cdna_length": 5077,
"mane_select": "ENST00000379942.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Pro789Ser",
"transcript": "ENST00000379942.5",
"protein_id": "ENSP00000369274.4",
"transcript_support_level": 1,
"aa_start": 789,
"aa_end": null,
"aa_length": 1235,
"cds_start": 2365,
"cds_end": null,
"cds_length": 3708,
"cdna_start": 2547,
"cdna_end": null,
"cdna_length": 5077,
"mane_select": "NM_000292.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Pro789Ser",
"transcript": "NM_001440805.1",
"protein_id": "NP_001427734.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 1243,
"cds_start": 2365,
"cds_end": null,
"cds_length": 3732,
"cdna_start": 2547,
"cdna_end": null,
"cdna_length": 5101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Pro789Ser",
"transcript": "NM_001440800.1",
"protein_id": "NP_001427729.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 1217,
"cds_start": 2365,
"cds_end": null,
"cds_length": 3654,
"cdna_start": 2547,
"cdna_end": null,
"cdna_length": 5023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Pro789Ser",
"transcript": "NM_001440801.1",
"protein_id": "NP_001427730.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 1207,
"cds_start": 2365,
"cds_end": null,
"cds_length": 3624,
"cdna_start": 2547,
"cdna_end": null,
"cdna_length": 4993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2266C>T",
"hgvs_p": "p.Pro756Ser",
"transcript": "NM_001440802.1",
"protein_id": "NP_001427731.1",
"transcript_support_level": null,
"aa_start": 756,
"aa_end": null,
"aa_length": 1202,
"cds_start": 2266,
"cds_end": null,
"cds_length": 3609,
"cdna_start": 2448,
"cdna_end": null,
"cdna_length": 4978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2266C>T",
"hgvs_p": "p.Pro756Ser",
"transcript": "NM_001440803.1",
"protein_id": "NP_001427732.1",
"transcript_support_level": null,
"aa_start": 756,
"aa_end": null,
"aa_length": 1184,
"cds_start": 2266,
"cds_end": null,
"cds_length": 3555,
"cdna_start": 2448,
"cdna_end": null,
"cdna_length": 4924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2266C>T",
"hgvs_p": "p.Pro756Ser",
"transcript": "NM_001440804.1",
"protein_id": "NP_001427733.1",
"transcript_support_level": null,
"aa_start": 756,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2266,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 2448,
"cdna_end": null,
"cdna_length": 4894,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.2266C>T",
"hgvs_p": "p.Pro756Ser",
"transcript": "XM_011545537.4",
"protein_id": "XP_011543839.1",
"transcript_support_level": null,
"aa_start": 756,
"aa_end": null,
"aa_length": 1210,
"cds_start": 2266,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 2448,
"cdna_end": null,
"cdna_length": 5002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.1819C>T",
"hgvs_p": "p.Pro607Ser",
"transcript": "XM_047442166.1",
"protein_id": "XP_047298122.1",
"transcript_support_level": null,
"aa_start": 607,
"aa_end": null,
"aa_length": 1061,
"cds_start": 1819,
"cds_end": null,
"cds_length": 3186,
"cdna_start": 2004,
"cdna_end": null,
"cdna_length": 4558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.1459C>T",
"hgvs_p": "p.Pro487Ser",
"transcript": "XM_017029580.3",
"protein_id": "XP_016885069.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 941,
"cds_start": 1459,
"cds_end": null,
"cds_length": 2826,
"cdna_start": 1565,
"cdna_end": null,
"cdna_length": 4119,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.Pro450Ser",
"transcript": "XM_011545538.4",
"protein_id": "XP_011543840.1",
"transcript_support_level": null,
"aa_start": 450,
"aa_end": null,
"aa_length": 904,
"cds_start": 1348,
"cds_end": null,
"cds_length": 2715,
"cdna_start": 1465,
"cdna_end": null,
"cdna_length": 4019,
"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": 22,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "n.2547C>T",
"hgvs_p": null,
"transcript": "XR_001755697.3",
"protein_id": null,
"transcript_support_level": null,
"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": 3464,
"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": 22,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"hgvs_c": "n.2547C>T",
"hgvs_p": null,
"transcript": "XR_950461.4",
"protein_id": null,
"transcript_support_level": null,
"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": 4716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHKA2",
"gene_hgnc_id": 8926,
"dbsnp": "rs138395800",
"frequency_reference_population": 0.000120763754,
"hom_count_reference_population": 35,
"allele_count_reference_population": 146,
"gnomad_exomes_af": 0.0000674602,
"gnomad_genomes_af": 0.000642691,
"gnomad_exomes_ac": 74,
"gnomad_genomes_ac": 72,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02571326494216919,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.435,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1477,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.62,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": "ENST00000379942.5",
"gene_symbol": "PHKA2",
"hgnc_id": 8926,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Pro789Ser"
}
],
"clinvar_disease": "Glycogen storage disease IXa1,PHKA2-related disorder,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not provided|Glycogen storage disease IXa1|PHKA2-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}