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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: 16-47596425-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=47596425&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 47596425,
"ref": "T",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000323584.10",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "c.1257T>A",
"hgvs_p": "p.Tyr419*",
"transcript": "NM_000293.3",
"protein_id": "NP_000284.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 1093,
"cds_start": 1257,
"cds_end": null,
"cds_length": 3282,
"cdna_start": 1277,
"cdna_end": null,
"cdna_length": 5459,
"mane_select": "ENST00000323584.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "c.1257T>A",
"hgvs_p": "p.Tyr419*",
"transcript": "ENST00000323584.10",
"protein_id": "ENSP00000313504.5",
"transcript_support_level": 1,
"aa_start": 419,
"aa_end": null,
"aa_length": 1093,
"cds_start": 1257,
"cds_end": null,
"cds_length": 3282,
"cdna_start": 1277,
"cdna_end": null,
"cdna_length": 5459,
"mane_select": "NM_000293.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "c.1236T>A",
"hgvs_p": "p.Tyr412*",
"transcript": "ENST00000566044.5",
"protein_id": "ENSP00000456729.1",
"transcript_support_level": 1,
"aa_start": 412,
"aa_end": null,
"aa_length": 1086,
"cds_start": 1236,
"cds_end": null,
"cds_length": 3261,
"cdna_start": 1425,
"cdna_end": null,
"cdna_length": 3829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "c.1257T>A",
"hgvs_p": "p.Tyr419*",
"transcript": "NM_001363837.1",
"protein_id": "NP_001350766.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 1093,
"cds_start": 1257,
"cds_end": null,
"cds_length": 3282,
"cdna_start": 1309,
"cdna_end": null,
"cdna_length": 5491,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "c.1257T>A",
"hgvs_p": "p.Tyr419*",
"transcript": "ENST00000299167.12",
"protein_id": "ENSP00000299167.8",
"transcript_support_level": 5,
"aa_start": 419,
"aa_end": null,
"aa_length": 1093,
"cds_start": 1257,
"cds_end": null,
"cds_length": 3282,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 5464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "c.1236T>A",
"hgvs_p": "p.Tyr412*",
"transcript": "NM_001031835.3",
"protein_id": "NP_001027005.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 1086,
"cds_start": 1236,
"cds_end": null,
"cds_length": 3261,
"cdna_start": 1389,
"cdna_end": null,
"cdna_length": 5571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "n.118T>A",
"hgvs_p": null,
"transcript": "ENST00000566436.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "n.1236T>A",
"hgvs_p": null,
"transcript": "ENST00000696809.1",
"protein_id": "ENSP00000512887.1",
"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": 4332,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "n.1236T>A",
"hgvs_p": null,
"transcript": "ENST00000699276.1",
"protein_id": "ENSP00000514257.1",
"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": 4492,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"hgvs_c": "c.-4T>A",
"hgvs_p": null,
"transcript": "ENST00000568439.1",
"protein_id": "ENSP00000458446.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 75,
"cds_start": -4,
"cds_end": null,
"cds_length": 228,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHKB",
"gene_hgnc_id": 8927,
"dbsnp": "rs121918021",
"frequency_reference_population": 0.000110419096,
"hom_count_reference_population": 0,
"allele_count_reference_population": 178,
"gnomad_exomes_af": 0.000114393,
"gnomad_genomes_af": 0.0000722923,
"gnomad_exomes_ac": 167,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.33000001311302185,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.51,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000323584.10",
"gene_symbol": "PHKB",
"hgnc_id": 8927,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1257T>A",
"hgvs_p": "p.Tyr419*"
}
],
"clinvar_disease": "Glycogen phosphorylase kinase deficiency,Glycogen storage disease IXb,PHKB-related disorder",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Glycogen storage disease IXb|Glycogen phosphorylase kinase deficiency|PHKB-related disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}