← Back to variant description
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-72582562-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=72582562&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 72582562,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000373542.9",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3334G>T",
"hgvs_p": "p.Glu1112*",
"transcript": "NM_002637.4",
"protein_id": "NP_002628.2",
"transcript_support_level": null,
"aa_start": 1112,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3334,
"cds_end": null,
"cds_length": 3672,
"cdna_start": 3760,
"cdna_end": null,
"cdna_length": 6286,
"mane_select": "ENST00000373542.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3334G>T",
"hgvs_p": "p.Glu1112*",
"transcript": "ENST00000373542.9",
"protein_id": "ENSP00000362643.4",
"transcript_support_level": 1,
"aa_start": 1112,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3334,
"cds_end": null,
"cds_length": 3672,
"cdna_start": 3760,
"cdna_end": null,
"cdna_length": 6286,
"mane_select": "NM_002637.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3295G>T",
"hgvs_p": "p.Glu1099*",
"transcript": "ENST00000339490.7",
"protein_id": "ENSP00000342469.3",
"transcript_support_level": 1,
"aa_start": 1099,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3295,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3596,
"cdna_end": null,
"cdna_length": 6121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3118G>T",
"hgvs_p": "p.Glu1040*",
"transcript": "ENST00000541944.5",
"protein_id": "ENSP00000441251.1",
"transcript_support_level": 1,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3118,
"cds_end": null,
"cds_length": 3456,
"cdna_start": 3419,
"cdna_end": null,
"cdna_length": 5944,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3385G>T",
"hgvs_p": "p.Glu1129*",
"transcript": "NM_001431068.1",
"protein_id": "NP_001417997.1",
"transcript_support_level": null,
"aa_start": 1129,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3385,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 3811,
"cdna_end": null,
"cdna_length": 6337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3385G>T",
"hgvs_p": "p.Glu1129*",
"transcript": "ENST00000373539.3",
"protein_id": "ENSP00000362640.3",
"transcript_support_level": 5,
"aa_start": 1129,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3385,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 3763,
"cdna_end": null,
"cdna_length": 4476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3295G>T",
"hgvs_p": "p.Glu1099*",
"transcript": "NM_001122670.2",
"protein_id": "NP_001116142.1",
"transcript_support_level": null,
"aa_start": 1099,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3295,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3721,
"cdna_end": null,
"cdna_length": 6247,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3295G>T",
"hgvs_p": "p.Glu1099*",
"transcript": "NM_001440787.1",
"protein_id": "NP_001427716.1",
"transcript_support_level": null,
"aa_start": 1099,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3295,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3612,
"cdna_end": null,
"cdna_length": 6138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3208G>T",
"hgvs_p": "p.Glu1070*",
"transcript": "ENST00000373545.7",
"protein_id": "ENSP00000362646.3",
"transcript_support_level": 5,
"aa_start": 1070,
"aa_end": null,
"aa_length": 1181,
"cds_start": 3208,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 3647,
"cdna_end": null,
"cdna_length": 6173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3118G>T",
"hgvs_p": "p.Glu1040*",
"transcript": "NM_001172436.2",
"protein_id": "NP_001165907.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3118,
"cds_end": null,
"cds_length": 3456,
"cdna_start": 3544,
"cdna_end": null,
"cdna_length": 6070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3118G>T",
"hgvs_p": "p.Glu1040*",
"transcript": "NM_001440788.1",
"protein_id": "NP_001427717.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3118,
"cds_end": null,
"cds_length": 3456,
"cdna_start": 3435,
"cdna_end": null,
"cdna_length": 5961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3334G>T",
"hgvs_p": "p.Glu1112*",
"transcript": "XM_047442160.1",
"protein_id": "XP_047298116.1",
"transcript_support_level": null,
"aa_start": 1112,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3334,
"cds_end": null,
"cds_length": 3672,
"cdna_start": 3651,
"cdna_end": null,
"cdna_length": 6177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3157G>T",
"hgvs_p": "p.Glu1053*",
"transcript": "XM_006724661.3",
"protein_id": "XP_006724724.1",
"transcript_support_level": null,
"aa_start": 1053,
"aa_end": null,
"aa_length": 1164,
"cds_start": 3157,
"cds_end": null,
"cds_length": 3495,
"cdna_start": 3583,
"cdna_end": null,
"cdna_length": 6109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"dbsnp": "rs137852546",
"frequency_reference_population": 0.0000074962954,
"hom_count_reference_population": 4,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000550956,
"gnomad_genomes_af": 0.0000268875,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5699999928474426,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9599999785423279,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.821,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.96,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP3_Moderate,PP5_Very_Strong,BS2_Supporting",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 1,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PP3_Moderate",
"PP5_Very_Strong",
"BS2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "ENST00000373542.9",
"gene_symbol": "PHKA1",
"hgnc_id": 8925,
"effects": [
"stop_gained"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.3334G>T",
"hgvs_p": "p.Glu1112*"
}
],
"clinvar_disease": "Glycogen storage disease IXd",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Glycogen storage disease IXd",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}