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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: 21-42486421-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=42486421&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 42486421,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000291536.8",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.315C>T",
"hgvs_p": "p.Tyr105Tyr",
"transcript": "NM_080860.4",
"protein_id": "NP_543136.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 309,
"cds_start": 315,
"cds_end": null,
"cds_length": 930,
"cdna_start": 353,
"cdna_end": null,
"cdna_length": 1300,
"mane_select": "ENST00000291536.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.315C>T",
"hgvs_p": "p.Tyr105Tyr",
"transcript": "ENST00000291536.8",
"protein_id": "ENSP00000291536.3",
"transcript_support_level": 1,
"aa_start": 105,
"aa_end": null,
"aa_length": 309,
"cds_start": 315,
"cds_end": null,
"cds_length": 930,
"cdna_start": 353,
"cdna_end": null,
"cdna_length": 1300,
"mane_select": "NM_080860.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.201C>T",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "NM_001286506.2",
"protein_id": "NP_001273435.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 271,
"cds_start": 201,
"cds_end": null,
"cds_length": 816,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 1186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.201C>T",
"hgvs_p": "p.Tyr67Tyr",
"transcript": "ENST00000398352.3",
"protein_id": "ENSP00000381395.3",
"transcript_support_level": 5,
"aa_start": 67,
"aa_end": null,
"aa_length": 271,
"cds_start": 201,
"cds_end": null,
"cds_length": 816,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.315C>T",
"hgvs_p": "p.Tyr105Tyr",
"transcript": "XM_011529786.2",
"protein_id": "XP_011528088.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 285,
"cds_start": 315,
"cds_end": null,
"cds_length": 858,
"cdna_start": 353,
"cdna_end": null,
"cdna_length": 1228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.108C>T",
"hgvs_p": "p.Tyr36Tyr",
"transcript": "XM_005261208.3",
"protein_id": "XP_005261265.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 240,
"cds_start": 108,
"cds_end": null,
"cds_length": 723,
"cdna_start": 146,
"cdna_end": null,
"cdna_length": 1093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "n.375C>T",
"hgvs_p": null,
"transcript": "ENST00000493019.1",
"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": 2880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"dbsnp": "rs144037391",
"frequency_reference_population": 0.00007558551,
"hom_count_reference_population": 0,
"allele_count_reference_population": 122,
"gnomad_exomes_af": 0.0000506237,
"gnomad_genomes_af": 0.000315167,
"gnomad_exomes_ac": 74,
"gnomad_genomes_ac": 48,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5099999904632568,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.135,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000291536.8",
"gene_symbol": "RSPH1",
"hgnc_id": 12371,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.315C>T",
"hgvs_p": "p.Tyr105Tyr"
}
],
"clinvar_disease": "Primary ciliary dyskinesia",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Primary ciliary dyskinesia",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}