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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: 9-95516816-TC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=95516816&ref=TC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 95516816,
"ref": "TC",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "NM_001083603.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.4delG",
"hgvs_p": "p.Glu2fs",
"transcript": "NM_001083603.3",
"protein_id": "NP_001077072.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 1446,
"cds_start": 4,
"cds_end": null,
"cds_length": 4341,
"cdna_start": 155,
"cdna_end": null,
"cdna_length": 7905,
"mane_select": null,
"mane_plus": "ENST00000437951.6",
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.4delG",
"hgvs_p": "p.Glu2fs",
"transcript": "ENST00000437951.6",
"protein_id": "ENSP00000389744.2",
"transcript_support_level": 5,
"aa_start": 2,
"aa_end": null,
"aa_length": 1446,
"cds_start": 4,
"cds_end": null,
"cds_length": 4341,
"cdna_start": 155,
"cdna_end": null,
"cdna_length": 7905,
"mane_select": null,
"mane_plus": "NM_001083603.3",
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.-346delG",
"hgvs_p": null,
"transcript": "ENST00000468211.6",
"protein_id": "ENSP00000449745.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 183,
"cds_start": -4,
"cds_end": null,
"cds_length": 552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.-346delG",
"hgvs_p": null,
"transcript": "NM_001083602.3",
"protein_id": "NP_001077071.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1381,
"cds_start": -4,
"cds_end": null,
"cds_length": 4146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.-346delG",
"hgvs_p": null,
"transcript": "ENST00000430669.6",
"protein_id": "ENSP00000410287.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1381,
"cds_start": -4,
"cds_end": null,
"cds_length": 4146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.-346delG",
"hgvs_p": null,
"transcript": "ENST00000711046.1",
"protein_id": "ENSP00000518556.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1381,
"cds_start": -4,
"cds_end": null,
"cds_length": 4146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.-346delG",
"hgvs_p": null,
"transcript": "NM_001354919.2",
"protein_id": "NP_001341848.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 183,
"cds_start": -4,
"cds_end": null,
"cds_length": 552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "n.-159delG",
"hgvs_p": null,
"transcript": "ENST00000551425.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "n.-159delG",
"hgvs_p": null,
"transcript": "ENST00000551623.1",
"protein_id": "ENSP00000447242.1",
"transcript_support_level": 1,
"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": 366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"dbsnp": "rs752765582",
"frequency_reference_population": 0.0000474711,
"hom_count_reference_population": 0,
"allele_count_reference_population": 76,
"gnomad_exomes_af": 0.0000496944,
"gnomad_genomes_af": 0.0000262954,
"gnomad_exomes_ac": 72,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.125,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1,BS2",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 4,
"pathogenic_score": 8,
"criteria": [
"PVS1",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001083603.3",
"gene_symbol": "PTCH1",
"hgnc_id": 9585,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4delG",
"hgvs_p": "p.Glu2fs"
}
],
"clinvar_disease": "Anophthalmia-microphthalmia syndrome,Gorlin syndrome,Hereditary cancer-predisposing syndrome,Holoprosencephaly 7",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:1 LB:1",
"phenotype_combined": "Anophthalmia-microphthalmia syndrome|Hereditary cancer-predisposing syndrome|Gorlin syndrome;Holoprosencephaly 7|Gorlin syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}