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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: X-71110951-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=71110951&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 71110951,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000374202.7",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Cys72Phe",
"transcript": "NM_000206.3",
"protein_id": "NP_000197.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 369,
"cds_start": 215,
"cds_end": null,
"cds_length": 1110,
"cdna_start": 253,
"cdna_end": null,
"cdna_length": 1480,
"mane_select": "ENST00000374202.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Cys72Phe",
"transcript": "ENST00000374202.7",
"protein_id": "ENSP00000363318.3",
"transcript_support_level": 1,
"aa_start": 72,
"aa_end": null,
"aa_length": 369,
"cds_start": 215,
"cds_end": null,
"cds_length": 1110,
"cdna_start": 253,
"cdna_end": null,
"cdna_length": 1480,
"mane_select": "NM_000206.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.215G>T",
"hgvs_p": null,
"transcript": "ENST00000646505.1",
"protein_id": "ENSP00000496673.1",
"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": 1920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Cys72Phe",
"transcript": "NM_001438870.1",
"protein_id": "NP_001425799.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 260,
"cds_start": 215,
"cds_end": null,
"cds_length": 783,
"cdna_start": 253,
"cdna_end": null,
"cdna_length": 1383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Cys72Phe",
"transcript": "ENST00000482750.6",
"protein_id": "ENSP00000421262.2",
"transcript_support_level": 5,
"aa_start": 72,
"aa_end": null,
"aa_length": 260,
"cds_start": 215,
"cds_end": null,
"cds_length": 783,
"cdna_start": 266,
"cdna_end": null,
"cdna_length": 1084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "c.83G>T",
"hgvs_p": "p.Cys28Phe",
"transcript": "ENST00000464642.5",
"protein_id": "ENSP00000425233.1",
"transcript_support_level": 5,
"aa_start": 28,
"aa_end": null,
"aa_length": 218,
"cds_start": 83,
"cds_end": null,
"cds_length": 659,
"cdna_start": 207,
"cdna_end": null,
"cdna_length": 783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "c.152G>T",
"hgvs_p": "p.Cys51Phe",
"transcript": "ENST00000473378.1",
"protein_id": "ENSP00000423601.1",
"transcript_support_level": 5,
"aa_start": 51,
"aa_end": null,
"aa_length": 98,
"cds_start": 152,
"cds_end": null,
"cds_length": 298,
"cdna_start": 258,
"cdna_end": null,
"cdna_length": 404,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "n.600G>T",
"hgvs_p": null,
"transcript": "ENST00000276110.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 2035,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "n.610G>T",
"hgvs_p": null,
"transcript": "ENST00000487883.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 959,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "n.282G>T",
"hgvs_p": null,
"transcript": "ENST00000512747.3",
"protein_id": null,
"transcript_support_level": 2,
"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": 1971,
"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": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.579G>T",
"hgvs_p": null,
"transcript": "ENST00000642473.1",
"protein_id": null,
"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": 1831,
"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": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.621G>T",
"hgvs_p": null,
"transcript": "ENST00000644022.1",
"protein_id": null,
"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": 1863,
"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": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.621G>T",
"hgvs_p": null,
"transcript": "ENST00000644708.1",
"protein_id": null,
"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": 1862,
"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": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.621G>T",
"hgvs_p": null,
"transcript": "ENST00000644911.1",
"protein_id": null,
"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": 1985,
"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": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.215G>T",
"hgvs_p": null,
"transcript": "ENST00000645266.1",
"protein_id": "ENSP00000493734.1",
"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": 1737,
"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": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.215G>T",
"hgvs_p": null,
"transcript": "ENST00000645518.1",
"protein_id": "ENSP00000493986.1",
"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": 1614,
"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": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.215G>T",
"hgvs_p": null,
"transcript": "ENST00000646106.1",
"protein_id": "ENSP00000496437.1",
"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": 1597,
"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": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285171",
"gene_hgnc_id": null,
"hgvs_c": "n.215G>T",
"hgvs_p": null,
"transcript": "ENST00000647492.1",
"protein_id": "ENSP00000495340.1",
"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": 1715,
"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": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"hgvs_c": "n.266G>T",
"hgvs_p": null,
"transcript": "ENST00000696903.1",
"protein_id": null,
"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": 1735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IL2RG",
"gene_hgnc_id": 6010,
"dbsnp": "rs1556330960",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9858598709106445,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.922,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9472,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.74,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.147,
"phylop100way_prediction": "Uncertain_significance",
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000374202.7",
"gene_symbol": "IL2RG",
"hgnc_id": 6010,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Cys72Phe"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000646505.1",
"gene_symbol": "ENSG00000285171",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.215G>T",
"hgvs_p": null
}
],
"clinvar_disease": "X-linked severe combined immunodeficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "X-linked severe combined immunodeficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}