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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: 11-66233031-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=66233031&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 66233031,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000320580.9",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PACS1",
"gene_hgnc_id": 30032,
"hgvs_c": "c.1803C>T",
"hgvs_p": "p.Ala601Ala",
"transcript": "NM_018026.4",
"protein_id": "NP_060496.2",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 963,
"cds_start": 1803,
"cds_end": null,
"cds_length": 2892,
"cdna_start": 2018,
"cdna_end": null,
"cdna_length": 4571,
"mane_select": "ENST00000320580.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PACS1",
"gene_hgnc_id": 30032,
"hgvs_c": "c.1803C>T",
"hgvs_p": "p.Ala601Ala",
"transcript": "ENST00000320580.9",
"protein_id": "ENSP00000316454.4",
"transcript_support_level": 1,
"aa_start": 601,
"aa_end": null,
"aa_length": 963,
"cds_start": 1803,
"cds_end": null,
"cds_length": 2892,
"cdna_start": 2018,
"cdna_end": null,
"cdna_length": 4571,
"mane_select": "NM_018026.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PACS1",
"gene_hgnc_id": 30032,
"hgvs_c": "c.411C>T",
"hgvs_p": "p.Ala137Ala",
"transcript": "ENST00000529757.5",
"protein_id": "ENSP00000432858.1",
"transcript_support_level": 1,
"aa_start": 137,
"aa_end": null,
"aa_length": 499,
"cds_start": 411,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 597,
"cdna_end": null,
"cdna_length": 1688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PACS1",
"gene_hgnc_id": 30032,
"hgvs_c": "c.-55C>T",
"hgvs_p": null,
"transcript": "ENST00000528935.1",
"protein_id": "ENSP00000437052.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 78,
"cds_start": -4,
"cds_end": null,
"cds_length": 237,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PACS1",
"gene_hgnc_id": 30032,
"hgvs_c": "c.1509C>T",
"hgvs_p": "p.Ala503Ala",
"transcript": "XM_011545162.2",
"protein_id": "XP_011543464.2",
"transcript_support_level": null,
"aa_start": 503,
"aa_end": null,
"aa_length": 865,
"cds_start": 1509,
"cds_end": null,
"cds_length": 2598,
"cdna_start": 1541,
"cdna_end": null,
"cdna_length": 4094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PACS1",
"gene_hgnc_id": 30032,
"hgvs_c": "c.1464C>T",
"hgvs_p": "p.Ala488Ala",
"transcript": "XM_011545164.3",
"protein_id": "XP_011543466.1",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 850,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2553,
"cdna_start": 1700,
"cdna_end": null,
"cdna_length": 4253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PACS1",
"gene_hgnc_id": 30032,
"hgvs_c": "c.-55C>T",
"hgvs_p": null,
"transcript": "ENST00000528935.1",
"protein_id": "ENSP00000437052.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 78,
"cds_start": -4,
"cds_end": null,
"cds_length": 237,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PACS1",
"gene_hgnc_id": 30032,
"dbsnp": "rs371400214",
"frequency_reference_population": 0.000010280014,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.00001028,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"computational_prediction_selected": "Benign",
"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": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.025,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000320580.9",
"gene_symbol": "PACS1",
"hgnc_id": 30032,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1803C>T",
"hgvs_p": "p.Ala601Ala"
}
],
"clinvar_disease": "Schuurs-Hoeijmakers syndrome,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not specified|Schuurs-Hoeijmakers syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}