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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: 19-29527234-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=29527234&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 29527234,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001146339.2",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM2B",
"gene_hgnc_id": 33595,
"hgvs_c": "c.106G>T",
"hgvs_p": "p.Asp36Tyr",
"transcript": "NM_001146339.2",
"protein_id": "NP_001139811.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 285,
"cds_start": 106,
"cds_end": null,
"cds_length": 858,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 2065,
"mane_select": "ENST00000335523.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM2B",
"gene_hgnc_id": 33595,
"hgvs_c": "c.106G>T",
"hgvs_p": "p.Asp36Tyr",
"transcript": "ENST00000335523.8",
"protein_id": "ENSP00000335038.6",
"transcript_support_level": 5,
"aa_start": 36,
"aa_end": null,
"aa_length": 285,
"cds_start": 106,
"cds_end": null,
"cds_length": 858,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 2065,
"mane_select": "NM_001146339.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM2B",
"gene_hgnc_id": 33595,
"hgvs_c": "c.106G>T",
"hgvs_p": "p.Asp36Tyr",
"transcript": "NM_001384640.1",
"protein_id": "NP_001371569.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 275,
"cds_start": 106,
"cds_end": null,
"cds_length": 828,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 2035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM2B",
"gene_hgnc_id": 33595,
"hgvs_c": "c.106G>T",
"hgvs_p": "p.Asp36Tyr",
"transcript": "XM_011526902.3",
"protein_id": "XP_011525204.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 285,
"cds_start": 106,
"cds_end": null,
"cds_length": 858,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 2236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM2B",
"gene_hgnc_id": 33595,
"hgvs_c": "c.106G>T",
"hgvs_p": "p.Asp36Tyr",
"transcript": "XM_011526903.3",
"protein_id": "XP_011525205.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 275,
"cds_start": 106,
"cds_end": null,
"cds_length": 828,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 2206,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM2B",
"gene_hgnc_id": 33595,
"hgvs_c": "c.-33G>T",
"hgvs_p": null,
"transcript": "NM_001384641.1",
"protein_id": "NP_001371570.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 239,
"cds_start": -4,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1633,
"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": "VSTM2B",
"gene_hgnc_id": 33595,
"hgvs_c": "c.-33G>T",
"hgvs_p": null,
"transcript": "NM_001384642.1",
"protein_id": "NP_001371571.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 229,
"cds_start": -4,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VSTM2B-DT",
"gene_hgnc_id": 27615,
"hgvs_c": "n.116+1807C>A",
"hgvs_p": null,
"transcript": "ENST00000804084.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VSTM2B-DT",
"gene_hgnc_id": 27615,
"hgvs_c": "n.116+1807C>A",
"hgvs_p": null,
"transcript": "ENST00000804085.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VSTM2B-DT",
"gene_hgnc_id": 27615,
"hgvs_c": "n.103+1478C>A",
"hgvs_p": null,
"transcript": "ENST00000804102.1",
"protein_id": null,
"transcript_support_level": null,
"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": 520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124904683",
"gene_hgnc_id": null,
"hgvs_c": "n.240+1807C>A",
"hgvs_p": null,
"transcript": "XR_007067215.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VSTM2B",
"gene_hgnc_id": 33595,
"dbsnp": "rs1257753562",
"frequency_reference_population": 0.000002146918,
"hom_count_reference_population": 1,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000214692,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7946591377258301,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.739,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9492,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.108,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001146339.2",
"gene_symbol": "VSTM2B",
"hgnc_id": 33595,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.106G>T",
"hgvs_p": "p.Asp36Tyr"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000804084.1",
"gene_symbol": "VSTM2B-DT",
"hgnc_id": 27615,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.116+1807C>A",
"hgvs_p": null
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007067215.1",
"gene_symbol": "LOC124904683",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.240+1807C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}