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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: 1-1203622-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1203622&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TNFRSF18",
"hgnc_id": 11914,
"hgvs_c": "c.737C>T",
"hgvs_p": "p.Ser246Phe",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_148901.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 4,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.151,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.19931858777999878,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 255,
"aa_ref": "S",
"aa_start": 246,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 851,
"cdna_start": 737,
"cds_end": null,
"cds_length": 768,
"cds_start": 737,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000328596.10",
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"hgvs_c": "c.737C>T",
"hgvs_p": "p.Ser246Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000328207.6",
"strand": false,
"transcript": "ENST00000328596.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 241,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1083,
"cdna_start": null,
"cds_end": null,
"cds_length": 726,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_004195.3",
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"hgvs_c": "c.*222C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000379268.7",
"protein_coding": true,
"protein_id": "NP_004186.1",
"strand": false,
"transcript": "NM_004195.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 241,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1083,
"cdna_start": null,
"cds_end": null,
"cds_length": 726,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000379268.7",
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"hgvs_c": "c.*222C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004195.3",
"protein_coding": true,
"protein_id": "ENSP00000368570.2",
"strand": false,
"transcript": "ENST00000379268.7",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 255,
"aa_ref": "S",
"aa_start": 246,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 872,
"cdna_start": 758,
"cds_end": null,
"cds_length": 768,
"cds_start": 737,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_148901.2",
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"hgvs_c": "c.737C>T",
"hgvs_p": "p.Ser246Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_683699.1",
"strand": false,
"transcript": "NM_148901.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 347,
"aa_ref": "S",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1148,
"cdna_start": 1034,
"cds_end": null,
"cds_length": 1044,
"cds_start": 1013,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017002722.3",
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"hgvs_c": "c.1013C>T",
"hgvs_p": "p.Ser338Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016858211.1",
"strand": false,
"transcript": "XM_017002722.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 234,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1062,
"cdna_start": null,
"cds_end": null,
"cds_length": 705,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_148902.2",
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"hgvs_c": "c.*222C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_683700.1",
"strand": false,
"transcript": "NM_148902.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 234,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 705,
"cdna_start": null,
"cds_end": null,
"cds_length": 705,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000379265.5",
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"hgvs_c": "c.*222C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000368567.5",
"strand": true,
"transcript": "ENST00000379265.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 169,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 727,
"cdna_start": null,
"cds_end": null,
"cds_length": 510,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000486728.5",
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"hgvs_c": "c.*222C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000462735.1",
"strand": true,
"transcript": "ENST00000486728.5",
"transcript_support_level": 1
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1224903237",
"effect": "missense_variant",
"frequency_reference_population": 0.000002608395,
"gene_hgnc_id": 11914,
"gene_symbol": "TNFRSF18",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.0000021719,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000656892,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.431,
"pos": 1203622,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.062,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_148901.2"
}
]
}