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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: 16-28933075-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28933075&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 28933075,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000538922.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "NM_001770.6",
"protein_id": "NP_001761.3",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 556,
"cds_start": 520,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 550,
"cdna_end": null,
"cdna_length": 1918,
"mane_select": "ENST00000538922.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000538922.8",
"protein_id": "ENSP00000437940.2",
"transcript_support_level": 5,
"aa_start": 174,
"aa_end": null,
"aa_length": 556,
"cds_start": 520,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 550,
"cdna_end": null,
"cdna_length": 1918,
"mane_select": "NM_001770.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "ENST00000324662.8",
"protein_id": "ENSP00000313419.4",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 557,
"cds_start": 520,
"cds_end": null,
"cds_length": 1674,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 1922,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "NM_001178098.2",
"protein_id": "NP_001171569.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 557,
"cds_start": 520,
"cds_end": null,
"cds_length": 1674,
"cdna_start": 550,
"cdna_end": null,
"cdna_length": 1921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.253C>G",
"hgvs_p": "p.Leu85Val",
"transcript": "NM_001385732.1",
"protein_id": "NP_001372661.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 467,
"cds_start": 253,
"cds_end": null,
"cds_length": 1404,
"cdna_start": 283,
"cdna_end": null,
"cdna_length": 1651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val",
"transcript": "XM_011545981.3",
"protein_id": "XP_011544283.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 282,
"cds_start": 520,
"cds_end": null,
"cds_length": 849,
"cdna_start": 550,
"cdna_end": null,
"cdna_length": 951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "n.854C>G",
"hgvs_p": null,
"transcript": "ENST00000565089.5",
"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": 2322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "n.143C>G",
"hgvs_p": null,
"transcript": "ENST00000566890.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "n.848C>G",
"hgvs_p": null,
"transcript": "NR_169755.1",
"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": 2230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "n.550C>G",
"hgvs_p": null,
"transcript": "XR_950871.3",
"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": 1154,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RABEP2",
"gene_hgnc_id": 24817,
"hgvs_c": "c.-150+3189G>C",
"hgvs_p": null,
"transcript": "ENST00000566762.1",
"protein_id": "ENSP00000454974.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 43,
"cds_start": -4,
"cds_end": null,
"cds_length": 133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"dbsnp": "rs2904880",
"frequency_reference_population": 0.7032779,
"hom_count_reference_population": 404691,
"allele_count_reference_population": 1134331,
"gnomad_exomes_af": 0.697006,
"gnomad_genomes_af": 0.763534,
"gnomad_exomes_ac": 1018231,
"gnomad_genomes_ac": 116100,
"gnomad_exomes_homalt": 359107,
"gnomad_genomes_homalt": 45584,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 7.500302672269754e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.072,
"revel_prediction": "Benign",
"alphamissense_score": 0.06,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.146,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000538922.8",
"gene_symbol": "CD19",
"hgnc_id": 1633,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.520C>G",
"hgvs_p": "p.Leu174Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000566762.1",
"gene_symbol": "RABEP2",
"hgnc_id": 24817,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-150+3189G>C",
"hgvs_p": null
}
],
"clinvar_disease": " 3, common variable,Immunodeficiency,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|Immunodeficiency, common variable, 3|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}