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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: 3-158105864-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=158105864&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 158105864,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001163678.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "NM_001163678.2",
"protein_id": "NP_001157150.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 319,
"cds_start": 161,
"cds_end": null,
"cds_length": 960,
"cdna_start": 557,
"cdna_end": null,
"cdna_length": 3478,
"mane_select": "ENST00000483851.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000483851.7",
"protein_id": "ENSP00000419362.1",
"transcript_support_level": 2,
"aa_start": 54,
"aa_end": null,
"aa_length": 319,
"cds_start": 161,
"cds_end": null,
"cds_length": 960,
"cdna_start": 557,
"cdna_end": null,
"cdna_length": 3478,
"mane_select": "NM_001163678.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000389589.8",
"protein_id": "ENSP00000374240.4",
"transcript_support_level": 1,
"aa_start": 54,
"aa_end": null,
"aa_length": 355,
"cds_start": 161,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 2072,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "NM_003030.4",
"protein_id": "NP_003021.3",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 355,
"cds_start": 161,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 3223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "NM_006884.3",
"protein_id": "NP_006875.2",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 331,
"cds_start": 161,
"cds_end": null,
"cds_length": 996,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 3151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000441443.6",
"protein_id": "ENSP00000397099.3",
"transcript_support_level": 5,
"aa_start": 54,
"aa_end": null,
"aa_length": 331,
"cds_start": 161,
"cds_end": null,
"cds_length": 996,
"cdna_start": 187,
"cdna_end": null,
"cdna_length": 3038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "XM_006713727.4",
"protein_id": "XP_006713790.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 343,
"cds_start": 161,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 557,
"cdna_end": null,
"cdna_length": 3550,
"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": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSRC1",
"gene_hgnc_id": 24152,
"hgvs_c": "c.-149G>A",
"hgvs_p": null,
"transcript": "ENST00000480820.5",
"protein_id": "ENSP00000420150.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 334,
"cds_start": -4,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"hgvs_c": "c.-148C>T",
"hgvs_p": null,
"transcript": "ENST00000554685.2",
"protein_id": "ENSP00000479329.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 144,
"cds_start": -4,
"cds_end": null,
"cds_length": 437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 439,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SHOX2",
"gene_hgnc_id": 10854,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3358866274356842,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.357,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1139,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.816,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001163678.2",
"gene_symbol": "SHOX2",
"hgnc_id": 10854,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000480820.5",
"gene_symbol": "RSRC1",
"hgnc_id": 24152,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-149G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}