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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: 5-123029312-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=123029312&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 123029312,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000943.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIC",
"gene_hgnc_id": 9256,
"hgvs_c": "c.224C>T",
"hgvs_p": "p.Thr75Ile",
"transcript": "NM_000943.5",
"protein_id": "NP_000934.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 212,
"cds_start": 224,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000306442.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000943.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIC",
"gene_hgnc_id": 9256,
"hgvs_c": "c.224C>T",
"hgvs_p": "p.Thr75Ile",
"transcript": "ENST00000306442.5",
"protein_id": "ENSP00000303057.4",
"transcript_support_level": 1,
"aa_start": 75,
"aa_end": null,
"aa_length": 212,
"cds_start": 224,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000943.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000306442.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIC",
"gene_hgnc_id": 9256,
"hgvs_c": "c.365C>T",
"hgvs_p": "p.Thr122Ile",
"transcript": "ENST00000910736.1",
"protein_id": "ENSP00000580795.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 259,
"cds_start": 365,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910736.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIC",
"gene_hgnc_id": 9256,
"hgvs_c": "c.224C>T",
"hgvs_p": "p.Thr75Ile",
"transcript": "ENST00000910735.1",
"protein_id": "ENSP00000580794.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 212,
"cds_start": 224,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910735.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIC",
"gene_hgnc_id": 9256,
"hgvs_c": "c.224C>T",
"hgvs_p": "p.Thr75Ile",
"transcript": "ENST00000953401.1",
"protein_id": "ENSP00000623460.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 202,
"cds_start": 224,
"cds_end": null,
"cds_length": 609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953401.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX24",
"gene_hgnc_id": 21533,
"hgvs_c": "c.*30G>A",
"hgvs_p": null,
"transcript": "XM_017009395.2",
"protein_id": "XP_016864884.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 130,
"cds_start": null,
"cds_end": null,
"cds_length": 393,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009395.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIC",
"gene_hgnc_id": 9256,
"hgvs_c": "n.324C>T",
"hgvs_p": null,
"transcript": "ENST00000415659.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000415659.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX24",
"gene_hgnc_id": 21533,
"hgvs_c": "n.458G>A",
"hgvs_p": null,
"transcript": "ENST00000502387.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000502387.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX24",
"gene_hgnc_id": 21533,
"hgvs_c": "n.494G>A",
"hgvs_p": null,
"transcript": "ENST00000510914.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000510914.5"
}
],
"gene_symbol": "PPIC",
"gene_hgnc_id": 9256,
"dbsnp": "rs780987113",
"frequency_reference_population": 0.00007497134,
"hom_count_reference_population": 0,
"allele_count_reference_population": 121,
"gnomad_exomes_af": 0.0000814098,
"gnomad_genomes_af": 0.0000131397,
"gnomad_exomes_ac": 119,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8115790486335754,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.466,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5358,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.602,
"phylop100way_prediction": "Pathogenic",
"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": "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_000943.5",
"gene_symbol": "PPIC",
"hgnc_id": 9256,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.224C>T",
"hgvs_p": "p.Thr75Ile"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000510914.5",
"gene_symbol": "SNX24",
"hgnc_id": 21533,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.494G>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
}