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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: 2-29328388-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=29328388&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 29328388,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004304.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.1376A>G",
"hgvs_p": "p.Gln459Arg",
"transcript": "NM_004304.5",
"protein_id": "NP_004295.2",
"transcript_support_level": null,
"aa_start": 459,
"aa_end": null,
"aa_length": 1620,
"cds_start": 1376,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 2303,
"cdna_end": null,
"cdna_length": 6240,
"mane_select": "ENST00000389048.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004304.5"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.1376A>G",
"hgvs_p": "p.Gln459Arg",
"transcript": "ENST00000389048.8",
"protein_id": "ENSP00000373700.3",
"transcript_support_level": 1,
"aa_start": 459,
"aa_end": null,
"aa_length": 1620,
"cds_start": 1376,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 2303,
"cdna_end": null,
"cdna_length": 6240,
"mane_select": "NM_004304.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389048.8"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.245A>G",
"hgvs_p": "p.Gln82Arg",
"transcript": "ENST00000618119.4",
"protein_id": "ENSP00000482733.1",
"transcript_support_level": 5,
"aa_start": 82,
"aa_end": null,
"aa_length": 1243,
"cds_start": 245,
"cds_end": null,
"cds_length": 3732,
"cdna_start": 712,
"cdna_end": null,
"cdna_length": 4646,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000618119.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286963",
"gene_hgnc_id": null,
"hgvs_c": "n.313T>C",
"hgvs_p": null,
"transcript": "ENST00000731706.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1225,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000731706.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "n.2303A>G",
"hgvs_p": null,
"transcript": "XR_001738688.3",
"protein_id": null,
"transcript_support_level": null,
"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": 3855,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001738688.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC101929386",
"gene_hgnc_id": null,
"hgvs_c": "n.201T>C",
"hgvs_p": null,
"transcript": "XR_939920.3",
"protein_id": null,
"transcript_support_level": null,
"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": 1327,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_939920.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286963",
"gene_hgnc_id": null,
"hgvs_c": "n.291+5860T>C",
"hgvs_p": null,
"transcript": "ENST00000655343.1",
"protein_id": null,
"transcript_support_level": null,
"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": 733,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000655343.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286963",
"gene_hgnc_id": null,
"hgvs_c": "n.380+5860T>C",
"hgvs_p": null,
"transcript": "ENST00000731703.1",
"protein_id": null,
"transcript_support_level": null,
"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": 921,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000731703.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286963",
"gene_hgnc_id": null,
"hgvs_c": "n.277+8415T>C",
"hgvs_p": null,
"transcript": "ENST00000731704.1",
"protein_id": null,
"transcript_support_level": null,
"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": 648,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000731704.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286963",
"gene_hgnc_id": null,
"hgvs_c": "n.351+5860T>C",
"hgvs_p": null,
"transcript": "ENST00000731705.1",
"protein_id": null,
"transcript_support_level": null,
"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": 717,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000731705.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LOC101929386",
"gene_hgnc_id": null,
"hgvs_c": "n.447+5860T>C",
"hgvs_p": null,
"transcript": "XR_007086263.1",
"protein_id": null,
"transcript_support_level": null,
"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": 889,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007086263.1"
}
],
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"dbsnp": "rs773380015",
"frequency_reference_population": 0.00004832492,
"hom_count_reference_population": 0,
"allele_count_reference_population": 78,
"gnomad_exomes_af": 0.0000513042,
"gnomad_genomes_af": 0.0000197104,
"gnomad_exomes_ac": 75,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.028551220893859863,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.268,
"revel_prediction": "Benign",
"alphamissense_score": 0.055,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.541,
"phylop100way_prediction": "Benign",
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004304.5",
"gene_symbol": "ALK",
"hgnc_id": 427,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1376A>G",
"hgvs_p": "p.Gln459Arg"
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000731706.1",
"gene_symbol": "ENSG00000286963",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.313T>C",
"hgvs_p": null
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "XR_939920.3",
"gene_symbol": "LOC101929386",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.201T>C",
"hgvs_p": null
}
],
"clinvar_disease": " 3, susceptibility to,ALK-related disorder,Hereditary cancer-predisposing syndrome,Neuroblastoma,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "Neuroblastoma, susceptibility to, 3|ALK-related disorder|Hereditary cancer-predisposing syndrome|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}