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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: 2-136115470-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=136115470&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CXCR4",
"hgnc_id": 2561,
"hgvs_c": "c.671A>C",
"hgvs_p": "p.Glu224Ala",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_001348056.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.2277,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " and myelokathexis, hypogammaglobulinemia, infections,Warts",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.23452961444854736,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 352,
"aa_ref": "E",
"aa_start": 153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1668,
"cdna_start": 547,
"cds_end": null,
"cds_length": 1059,
"cds_start": 458,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_003467.3",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.458A>C",
"hgvs_p": "p.Glu153Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000241393.4",
"protein_coding": true,
"protein_id": "NP_003458.1",
"strand": false,
"transcript": "NM_003467.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 352,
"aa_ref": "E",
"aa_start": 153,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1668,
"cdna_start": 547,
"cds_end": null,
"cds_length": 1059,
"cds_start": 458,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000241393.4",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.458A>C",
"hgvs_p": "p.Glu153Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003467.3",
"protein_coding": true,
"protein_id": "ENSP00000241393.3",
"strand": false,
"transcript": "ENST00000241393.4",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 337,
"aa_ref": "E",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1485,
"cdna_start": 652,
"cds_end": null,
"cds_length": 1014,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000466288.1",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.413A>C",
"hgvs_p": "p.Glu138Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512430.1",
"strand": false,
"transcript": "ENST00000466288.1",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 423,
"aa_ref": "E",
"aa_start": 224,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1881,
"cdna_start": 760,
"cds_end": null,
"cds_length": 1272,
"cds_start": 671,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001348056.2",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.671A>C",
"hgvs_p": "p.Glu224Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001334985.1",
"strand": false,
"transcript": "NM_001348056.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 385,
"aa_ref": "E",
"aa_start": 186,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1767,
"cdna_start": 646,
"cds_end": null,
"cds_length": 1158,
"cds_start": 557,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001348059.2",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.557A>C",
"hgvs_p": "p.Glu186Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001334988.1",
"strand": false,
"transcript": "NM_001348059.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 356,
"aa_ref": "E",
"aa_start": 157,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1887,
"cdna_start": 766,
"cds_end": null,
"cds_length": 1071,
"cds_start": 470,
"consequences": [
"missense_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001008540.2",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.470A>C",
"hgvs_p": "p.Glu157Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001008540.1",
"strand": false,
"transcript": "NM_001008540.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 356,
"aa_ref": "E",
"aa_start": 157,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1895,
"cdna_start": 774,
"cds_end": null,
"cds_length": 1071,
"cds_start": 470,
"consequences": [
"missense_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000409817.1",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.470A>C",
"hgvs_p": "p.Glu157Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386884.1",
"strand": false,
"transcript": "ENST00000409817.1",
"transcript_support_level": 6
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 348,
"aa_ref": "E",
"aa_start": 149,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1638,
"cdna_start": 517,
"cds_end": null,
"cds_length": 1047,
"cds_start": 446,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000696136.1",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.446A>C",
"hgvs_p": "p.Glu149Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512428.1",
"strand": false,
"transcript": "ENST00000696136.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 348,
"aa_ref": "E",
"aa_start": 149,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1787,
"cdna_start": 666,
"cds_end": null,
"cds_length": 1047,
"cds_start": 446,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000696228.1",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.446A>C",
"hgvs_p": "p.Glu149Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512494.1",
"strand": false,
"transcript": "ENST00000696228.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 337,
"aa_ref": "E",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1905,
"cdna_start": 784,
"cds_end": null,
"cds_length": 1014,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001348060.2",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.413A>C",
"hgvs_p": "p.Glu138Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001334989.1",
"strand": false,
"transcript": "NM_001348060.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 337,
"aa_ref": "E",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2170,
"cdna_start": 1049,
"cds_end": null,
"cds_length": 1014,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000696137.1",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.413A>C",
"hgvs_p": "p.Glu138Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512429.1",
"strand": false,
"transcript": "ENST00000696137.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 337,
"aa_ref": "E",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1666,
"cdna_start": 545,
"cds_end": null,
"cds_length": 1014,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000696152.1",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.413A>C",
"hgvs_p": "p.Glu138Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512443.1",
"strand": false,
"transcript": "ENST00000696152.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 436,
"aa_ref": "E",
"aa_start": 237,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2062,
"cdna_start": 941,
"cds_end": null,
"cds_length": 1311,
"cds_start": 710,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047445802.1",
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"hgvs_c": "c.710A>C",
"hgvs_p": "p.Glu237Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301758.1",
"strand": false,
"transcript": "XM_047445802.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1553457905",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 2561,
"gene_symbol": "CXCR4",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Warts, hypogammaglobulinemia, infections, and myelokathexis",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.143,
"pos": 136115470,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.095,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001348056.2"
}
]
}