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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: 12-102877464-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=102877464&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 102877464,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000553106.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.439C>T",
"hgvs_p": "p.Pro147Ser",
"transcript": "NM_000277.3",
"protein_id": "NP_000268.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 452,
"cds_start": 439,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 3759,
"mane_select": "ENST00000553106.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.439C>T",
"hgvs_p": "p.Pro147Ser",
"transcript": "ENST00000553106.6",
"protein_id": "ENSP00000448059.1",
"transcript_support_level": 1,
"aa_start": 147,
"aa_end": null,
"aa_length": 452,
"cds_start": 439,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 3759,
"mane_select": "NM_000277.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"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.535C>T",
"hgvs_p": null,
"transcript": "ENST00000549111.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1252,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.421C>T",
"hgvs_p": "p.Pro141Ser",
"transcript": "ENST00000550978.6",
"protein_id": "ENSP00000489016.1",
"transcript_support_level": 2,
"aa_start": 141,
"aa_end": null,
"aa_length": 148,
"cds_start": 421,
"cds_end": null,
"cds_length": 447,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 652,
"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",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.439C>T",
"hgvs_p": "p.Pro147Ser",
"transcript": "NM_001354304.2",
"protein_id": "NP_001341233.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 452,
"cds_start": 439,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 781,
"cdna_end": null,
"cdna_length": 3987,
"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",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.Pro142Ser",
"transcript": "ENST00000307000.7",
"protein_id": "ENSP00000303500.2",
"transcript_support_level": 5,
"aa_start": 142,
"aa_end": null,
"aa_length": 447,
"cds_start": 424,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 695,
"cdna_end": null,
"cdna_length": 2466,
"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",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.439C>T",
"hgvs_p": "p.Pro147Ser",
"transcript": "XM_017019370.2",
"protein_id": "XP_016874859.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 240,
"cds_start": 439,
"cds_end": null,
"cds_length": 723,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 1794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"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.528C>T",
"hgvs_p": null,
"transcript": "ENST00000551988.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124902999",
"gene_hgnc_id": null,
"hgvs_c": "n.808-2415G>A",
"hgvs_p": null,
"transcript": "XR_007063428.1",
"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": 1160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"hgvs_c": "c.*31C>T",
"hgvs_p": null,
"transcript": "ENST00000551337.5",
"protein_id": "ENSP00000447620.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 135,
"cds_start": -4,
"cds_end": null,
"cds_length": 408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PAH",
"gene_hgnc_id": 8582,
"dbsnp": "rs199475624",
"frequency_reference_population": 0.0000020550112,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205501,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9957966804504395,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.7960000038146973,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.96,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9313,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.183,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999026596771683,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP3,PM3_Strong,PP4_Moderate,PM2",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PP3",
"PM3_Strong",
"PP4_Moderate",
"PM2"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000553106.6",
"gene_symbol": "PAH",
"hgnc_id": 8582,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.439C>T",
"hgvs_p": "p.Pro147Ser"
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XR_007063428.1",
"gene_symbol": "LOC124902999",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.808-2415G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Phenylketonuria,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:4 LP:2 O:1",
"phenotype_combined": "not provided|Phenylketonuria",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}