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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: 12-102840473-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=102840473&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 102840473,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_000277.3",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Tyr414Tyr",
"transcript": "NM_000277.3",
"protein_id": "NP_000268.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 452,
"cds_start": 1242,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000553106.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000277.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Tyr414Tyr",
"transcript": "ENST00000553106.6",
"protein_id": "ENSP00000448059.1",
"transcript_support_level": 1,
"aa_start": 414,
"aa_end": null,
"aa_length": 452,
"cds_start": 1242,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000277.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000553106.6"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1341C>T",
"hgvs_p": "p.Tyr447Tyr",
"transcript": "ENST00000906695.1",
"protein_id": "ENSP00000576754.1",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 485,
"cds_start": 1341,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906695.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1320C>T",
"hgvs_p": "p.Tyr440Tyr",
"transcript": "ENST00000906692.1",
"protein_id": "ENSP00000576751.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 478,
"cds_start": 1320,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906692.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1260C>T",
"hgvs_p": "p.Tyr420Tyr",
"transcript": "ENST00000906694.1",
"protein_id": "ENSP00000576753.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 458,
"cds_start": 1260,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906694.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Tyr414Tyr",
"transcript": "NM_001354304.2",
"protein_id": "NP_001341233.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 452,
"cds_start": 1242,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354304.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Tyr414Tyr",
"transcript": "ENST00000906693.1",
"protein_id": "ENSP00000576752.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 452,
"cds_start": 1242,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906693.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1227C>T",
"hgvs_p": "p.Tyr409Tyr",
"transcript": "ENST00000307000.7",
"protein_id": "ENSP00000303500.2",
"transcript_support_level": 5,
"aa_start": 409,
"aa_end": null,
"aa_length": 447,
"cds_start": 1227,
"cds_end": null,
"cds_length": 1344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307000.7"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1134C>T",
"hgvs_p": "p.Tyr378Tyr",
"transcript": "ENST00000906696.1",
"protein_id": "ENSP00000576755.1",
"transcript_support_level": null,
"aa_start": 378,
"aa_end": null,
"aa_length": 416,
"cds_start": 1134,
"cds_end": null,
"cds_length": 1251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906696.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.969C>T",
"hgvs_p": "p.Tyr323Tyr",
"transcript": "ENST00000906697.1",
"protein_id": "ENSP00000576756.1",
"transcript_support_level": null,
"aa_start": 323,
"aa_end": null,
"aa_length": 361,
"cds_start": 969,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906697.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.345C>T",
"hgvs_p": "p.Tyr115Tyr",
"transcript": "ENST00000635477.1",
"protein_id": "ENSP00000489230.1",
"transcript_support_level": 5,
"aa_start": 115,
"aa_end": null,
"aa_length": 141,
"cds_start": 345,
"cds_end": null,
"cds_length": 428,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635477.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "n.904C>T",
"hgvs_p": null,
"transcript": "ENST00000551114.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000551114.2"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "n.757C>T",
"hgvs_p": null,
"transcript": "ENST00000635528.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000635528.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "n.*40C>T",
"hgvs_p": null,
"transcript": "ENST00000549247.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000549247.6"
}
],
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"dbsnp": "rs1801152",
"frequency_reference_population": 0.011549053,
"hom_count_reference_population": 143,
"allele_count_reference_population": 18638,
"gnomad_exomes_af": 0.0119635,
"gnomad_genomes_af": 0.00757148,
"gnomad_exomes_ac": 17485,
"gnomad_genomes_ac": 1153,
"gnomad_exomes_homalt": 139,
"gnomad_genomes_homalt": 4,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6200000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.433,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BS2,BS1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BS2",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_000277.3",
"gene_symbol": "PAH",
"hgnc_id": 8582,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Tyr414Tyr"
}
],
"clinvar_disease": "Phenylketonuria,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "B:10 O:1",
"phenotype_combined": "not provided|not specified|Phenylketonuria",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}