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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: 12-102843665-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=102843665&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 102843665,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000277.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1180G>C",
"hgvs_p": "p.Asp394His",
"transcript": "NM_000277.3",
"protein_id": "NP_000268.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 452,
"cds_start": 1180,
"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": "D",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1180G>C",
"hgvs_p": "p.Asp394His",
"transcript": "ENST00000553106.6",
"protein_id": "ENSP00000448059.1",
"transcript_support_level": 1,
"aa_start": 394,
"aa_end": null,
"aa_length": 452,
"cds_start": 1180,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1279G>C",
"hgvs_p": "p.Asp427His",
"transcript": "ENST00000906695.1",
"protein_id": "ENSP00000576754.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 485,
"cds_start": 1279,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1258G>C",
"hgvs_p": "p.Asp420His",
"transcript": "ENST00000906692.1",
"protein_id": "ENSP00000576751.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 478,
"cds_start": 1258,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1198G>C",
"hgvs_p": "p.Asp400His",
"transcript": "ENST00000906694.1",
"protein_id": "ENSP00000576753.1",
"transcript_support_level": null,
"aa_start": 400,
"aa_end": null,
"aa_length": 458,
"cds_start": 1198,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1180G>C",
"hgvs_p": "p.Asp394His",
"transcript": "NM_001354304.2",
"protein_id": "NP_001341233.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 452,
"cds_start": 1180,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1180G>C",
"hgvs_p": "p.Asp394His",
"transcript": "ENST00000906693.1",
"protein_id": "ENSP00000576752.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 452,
"cds_start": 1180,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1165G>C",
"hgvs_p": "p.Asp389His",
"transcript": "ENST00000307000.7",
"protein_id": "ENSP00000303500.2",
"transcript_support_level": 5,
"aa_start": 389,
"aa_end": null,
"aa_length": 447,
"cds_start": 1165,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.1072G>C",
"hgvs_p": "p.Asp358His",
"transcript": "ENST00000906696.1",
"protein_id": "ENSP00000576755.1",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 416,
"cds_start": 1072,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.907G>C",
"hgvs_p": "p.Asp303His",
"transcript": "ENST00000906697.1",
"protein_id": "ENSP00000576756.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 361,
"cds_start": 907,
"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": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.283G>C",
"hgvs_p": "p.Asp95His",
"transcript": "ENST00000635477.1",
"protein_id": "ENSP00000489230.1",
"transcript_support_level": 5,
"aa_start": 95,
"aa_end": null,
"aa_length": 141,
"cds_start": 283,
"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.939G>C",
"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"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "n.842G>C",
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "n.695G>C",
"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"
}
],
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"dbsnp": "rs62516142",
"frequency_reference_population": 0.0000013683447,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136834,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9819720983505249,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.913,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2549,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.5,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.015,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.09,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP3,PM3,PP4_Moderate,PM2",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PP3",
"PM3",
"PP4_Moderate",
"PM2"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000277.3",
"gene_symbol": "PAH",
"hgnc_id": 8582,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1180G>C",
"hgvs_p": "p.Asp394His"
}
],
"clinvar_disease": "Phenylketonuria,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:3 LP:2 O:1",
"phenotype_combined": "not provided|Phenylketonuria",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}