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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: 4-54013896-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=54013896&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 54013896,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_012110.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIC2",
"gene_hgnc_id": 1935,
"hgvs_c": "c.388C>T",
"hgvs_p": "p.Leu130Leu",
"transcript": "NM_012110.4",
"protein_id": "NP_036242.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 165,
"cds_start": 388,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263921.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012110.4"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIC2",
"gene_hgnc_id": 1935,
"hgvs_c": "c.388C>T",
"hgvs_p": "p.Leu130Leu",
"transcript": "ENST00000263921.8",
"protein_id": "ENSP00000263921.3",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 165,
"cds_start": 388,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012110.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263921.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ENSG00000282278",
"gene_hgnc_id": null,
"hgvs_c": "c.1018-261029G>A",
"hgvs_p": null,
"transcript": "ENST00000507166.5",
"protein_id": "ENSP00000423325.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 849,
"cds_start": null,
"cds_end": null,
"cds_length": 2550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507166.5"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIC2",
"gene_hgnc_id": 1935,
"hgvs_c": "c.331C>T",
"hgvs_p": "p.Leu111Leu",
"transcript": "ENST00000512964.5",
"protein_id": "ENSP00000425238.1",
"transcript_support_level": 5,
"aa_start": 111,
"aa_end": null,
"aa_length": 146,
"cds_start": 331,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512964.5"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIC2",
"gene_hgnc_id": 1935,
"hgvs_c": "c.301C>T",
"hgvs_p": "p.Leu101Leu",
"transcript": "ENST00000510894.2",
"protein_id": "ENSP00000421032.1",
"transcript_support_level": 2,
"aa_start": 101,
"aa_end": null,
"aa_length": 136,
"cds_start": 301,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000510894.2"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIC2",
"gene_hgnc_id": 1935,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Leu102Leu",
"transcript": "XM_006714037.5",
"protein_id": "XP_006714100.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 137,
"cds_start": 304,
"cds_end": null,
"cds_length": 414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006714037.5"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHIC2",
"gene_hgnc_id": 1935,
"hgvs_c": "c.280C>T",
"hgvs_p": "p.Leu94Leu",
"transcript": "XM_047450063.1",
"protein_id": "XP_047306019.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 129,
"cds_start": 280,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047450063.1"
}
],
"gene_symbol": "CHIC2",
"gene_hgnc_id": 1935,
"dbsnp": "rs150857189",
"frequency_reference_population": 0.00040353925,
"hom_count_reference_population": 0,
"allele_count_reference_population": 651,
"gnomad_exomes_af": 0.000413419,
"gnomad_genomes_af": 0.000308727,
"gnomad_exomes_ac": 604,
"gnomad_genomes_ac": 47,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3790000081062317,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.28600001335144043,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.379,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.71,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0150780607884323,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_012110.4",
"gene_symbol": "CHIC2",
"hgnc_id": 1935,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.388C>T",
"hgvs_p": "p.Leu130Leu"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000507166.5",
"gene_symbol": "ENSG00000282278",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1018-261029G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}