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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: 4-150916647-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=150916647&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 150916647,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000651943.2",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "NM_001364905.1",
"protein_id": "NP_001351834.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2852,
"cds_start": 737,
"cds_end": null,
"cds_length": 8559,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 10148,
"mane_select": "ENST00000651943.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "ENST00000651943.2",
"protein_id": "ENSP00000498582.2",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2852,
"cds_start": 737,
"cds_end": null,
"cds_length": 8559,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 10148,
"mane_select": "NM_001364905.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "ENST00000357115.9",
"protein_id": "ENSP00000349629.3",
"transcript_support_level": 1,
"aa_start": 246,
"aa_end": null,
"aa_length": 2863,
"cds_start": 737,
"cds_end": null,
"cds_length": 8592,
"cdna_start": 1211,
"cdna_end": null,
"cdna_length": 10353,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "ENST00000510413.5",
"protein_id": "ENSP00000421552.1",
"transcript_support_level": 1,
"aa_start": 246,
"aa_end": null,
"aa_length": 2851,
"cds_start": 737,
"cds_end": null,
"cds_length": 8556,
"cdna_start": 1022,
"cdna_end": null,
"cdna_length": 10032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "NM_001440430.1",
"protein_id": "NP_001427359.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2868,
"cds_start": 737,
"cds_end": null,
"cds_length": 8607,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 10196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "NM_006726.5",
"protein_id": "NP_006717.2",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2863,
"cds_start": 737,
"cds_end": null,
"cds_length": 8592,
"cdna_start": 1211,
"cdna_end": null,
"cdna_length": 10353,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "NM_001367550.1",
"protein_id": "NP_001354479.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2857,
"cds_start": 737,
"cds_end": null,
"cds_length": 8574,
"cdna_start": 1211,
"cdna_end": null,
"cdna_length": 10335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "NM_001440431.1",
"protein_id": "NP_001427360.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2857,
"cds_start": 737,
"cds_end": null,
"cds_length": 8574,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 10163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "ENST00000651695.2",
"protein_id": "ENSP00000498254.2",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2857,
"cds_start": 737,
"cds_end": null,
"cds_length": 8574,
"cdna_start": 988,
"cdna_end": null,
"cdna_length": 9880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "NM_001199282.3",
"protein_id": "NP_001186211.2",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2851,
"cds_start": 737,
"cds_end": null,
"cds_length": 8556,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 10145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "ENST00000507224.5",
"protein_id": "ENSP00000422180.1",
"transcript_support_level": 5,
"aa_start": 246,
"aa_end": null,
"aa_length": 2575,
"cds_start": 737,
"cds_end": null,
"cds_length": 7728,
"cdna_start": 1032,
"cdna_end": null,
"cdna_length": 8826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "XM_005263373.4",
"protein_id": "XP_005263430.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2868,
"cds_start": 737,
"cds_end": null,
"cds_length": 8607,
"cdna_start": 1211,
"cdna_end": null,
"cdna_length": 10368,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "XM_011532434.3",
"protein_id": "XP_011530736.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2863,
"cds_start": 737,
"cds_end": null,
"cds_length": 8592,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 10181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser",
"transcript": "XM_047416462.1",
"protein_id": "XP_047272418.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 2852,
"cds_start": 737,
"cds_end": null,
"cds_length": 8559,
"cdna_start": 1211,
"cdna_end": null,
"cdna_length": 10320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"hgvs_c": "n.737A>G",
"hgvs_p": null,
"transcript": "ENST00000651035.1",
"protein_id": "ENSP00000498673.1",
"transcript_support_level": null,
"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": 9674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LRBA",
"gene_hgnc_id": 1742,
"dbsnp": "rs753938783",
"frequency_reference_population": 0.000029388371,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000310977,
"gnomad_genomes_af": 0.0000131389,
"gnomad_exomes_ac": 45,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.42777132987976074,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1599999964237213,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.4,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0979,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.017,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.16,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000651943.2",
"gene_symbol": "LRBA",
"hgnc_id": 1742,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Asn246Ser"
}
],
"clinvar_disease": "Combined immunodeficiency due to LRBA deficiency,Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Combined immunodeficiency due to LRBA deficiency|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}