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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: 4-39300409-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=39300409&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 39300409,
"ref": "T",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000349703.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2541A>T",
"hgvs_p": "p.Pro847Pro",
"transcript": "NM_002913.5",
"protein_id": "NP_002904.3",
"transcript_support_level": null,
"aa_start": 847,
"aa_end": null,
"aa_length": 1147,
"cds_start": 2541,
"cds_end": null,
"cds_length": 3444,
"cdna_start": 2662,
"cdna_end": null,
"cdna_length": 4870,
"mane_select": "ENST00000349703.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2541A>T",
"hgvs_p": "p.Pro847Pro",
"transcript": "ENST00000349703.7",
"protein_id": "ENSP00000261424.4",
"transcript_support_level": 1,
"aa_start": 847,
"aa_end": null,
"aa_length": 1147,
"cds_start": 2541,
"cds_end": null,
"cds_length": 3444,
"cdna_start": 2662,
"cdna_end": null,
"cdna_length": 4870,
"mane_select": "NM_002913.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2544A>T",
"hgvs_p": "p.Pro848Pro",
"transcript": "ENST00000381897.5",
"protein_id": "ENSP00000371321.1",
"transcript_support_level": 1,
"aa_start": 848,
"aa_end": null,
"aa_length": 1148,
"cds_start": 2544,
"cds_end": null,
"cds_length": 3447,
"cdna_start": 2678,
"cdna_end": null,
"cdna_length": 4886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2544A>T",
"hgvs_p": "p.Pro848Pro",
"transcript": "NM_001204747.2",
"protein_id": "NP_001191676.1",
"transcript_support_level": null,
"aa_start": 848,
"aa_end": null,
"aa_length": 1148,
"cds_start": 2544,
"cds_end": null,
"cds_length": 3447,
"cdna_start": 2665,
"cdna_end": null,
"cdna_length": 4873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2466A>T",
"hgvs_p": "p.Pro822Pro",
"transcript": "NM_001363496.2",
"protein_id": "NP_001350425.1",
"transcript_support_level": null,
"aa_start": 822,
"aa_end": null,
"aa_length": 1122,
"cds_start": 2466,
"cds_end": null,
"cds_length": 3369,
"cdna_start": 2587,
"cdna_end": null,
"cdna_length": 4795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2463A>T",
"hgvs_p": "p.Pro821Pro",
"transcript": "NM_001363495.2",
"protein_id": "NP_001350424.1",
"transcript_support_level": null,
"aa_start": 821,
"aa_end": null,
"aa_length": 1121,
"cds_start": 2463,
"cds_end": null,
"cds_length": 3366,
"cdna_start": 2584,
"cdna_end": null,
"cdna_length": 4792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.2034A>T",
"hgvs_p": "p.Pro678Pro",
"transcript": "XM_011513731.2",
"protein_id": "XP_011512033.1",
"transcript_support_level": null,
"aa_start": 678,
"aa_end": null,
"aa_length": 978,
"cds_start": 2034,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 2155,
"cdna_end": null,
"cdna_length": 4363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "c.1956A>T",
"hgvs_p": "p.Pro652Pro",
"transcript": "XM_047416054.1",
"protein_id": "XP_047272010.1",
"transcript_support_level": null,
"aa_start": 652,
"aa_end": null,
"aa_length": 952,
"cds_start": 1956,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 2077,
"cdna_end": null,
"cdna_length": 4285,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"hgvs_c": "n.473A>T",
"hgvs_p": null,
"transcript": "ENST00000505077.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RFC1",
"gene_hgnc_id": 9969,
"dbsnp": "rs2066786",
"frequency_reference_population": 0.000004959444,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000479087,
"gnomad_genomes_af": 0.00000658016,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6600000262260437,
"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": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.951,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000349703.7",
"gene_symbol": "RFC1",
"hgnc_id": 9969,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2541A>T",
"hgvs_p": "p.Pro847Pro"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}