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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: 2-29197684-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=29197684&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 29197684,
"ref": "T",
"alt": "C",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000389048.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.3939-8A>G",
"hgvs_p": null,
"transcript": "NM_004304.5",
"protein_id": "NP_004295.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1620,
"cds_start": -4,
"cds_end": null,
"cds_length": 4863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6240,
"mane_select": "ENST00000389048.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.3939-8A>G",
"hgvs_p": null,
"transcript": "ENST00000389048.8",
"protein_id": "ENSP00000373700.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1620,
"cds_start": -4,
"cds_end": null,
"cds_length": 4863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6240,
"mane_select": "NM_004304.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "n.816-8A>G",
"hgvs_p": null,
"transcript": "ENST00000638605.1",
"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": 1757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLIP4",
"gene_hgnc_id": 26108,
"hgvs_c": "c.*678T>C",
"hgvs_p": null,
"transcript": "ENST00000689605.1",
"protein_id": "ENSP00000508948.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 666,
"cds_start": -4,
"cds_end": null,
"cds_length": 2001,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4963,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.2808-8A>G",
"hgvs_p": null,
"transcript": "ENST00000618119.4",
"protein_id": "ENSP00000482733.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1243,
"cds_start": -4,
"cds_end": null,
"cds_length": 3732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.735-8A>G",
"hgvs_p": null,
"transcript": "NM_001353765.2",
"protein_id": "NP_001340694.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 552,
"cds_start": -4,
"cds_end": null,
"cds_length": 1659,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.735-8A>G",
"hgvs_p": null,
"transcript": "ENST00000642122.1",
"protein_id": "ENSP00000493203.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 552,
"cds_start": -4,
"cds_end": null,
"cds_length": 1659,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "n.*778-8A>G",
"hgvs_p": null,
"transcript": "ENST00000431873.6",
"protein_id": "ENSP00000414027.3",
"transcript_support_level": 5,
"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": 2520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"dbsnp": "rs3738869",
"frequency_reference_population": 0.00063044275,
"hom_count_reference_population": 8,
"allele_count_reference_population": 1017,
"gnomad_exomes_af": 0.000609867,
"gnomad_genomes_af": 0.000827978,
"gnomad_exomes_ac": 891,
"gnomad_genomes_ac": 126,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.378,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000364494159461684,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000389048.8",
"gene_symbol": "ALK",
"hgnc_id": 427,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3939-8A>G",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000689605.1",
"gene_symbol": "CLIP4",
"hgnc_id": 26108,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*678T>C",
"hgvs_p": null
}
],
"clinvar_disease": " 3, susceptibility to,Neuroblastoma,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:4",
"phenotype_combined": "Neuroblastoma, susceptibility to, 3|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}