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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: 16-28932061-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28932061&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 28932061,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001178098.2",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.61G>C",
"hgvs_p": "p.Glu21Gln",
"transcript": "NM_001770.6",
"protein_id": "NP_001761.3",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 556,
"cds_start": 61,
"cds_end": null,
"cds_length": 1671,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000538922.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001770.6"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.61G>C",
"hgvs_p": "p.Glu21Gln",
"transcript": "ENST00000538922.8",
"protein_id": "ENSP00000437940.2",
"transcript_support_level": 5,
"aa_start": 21,
"aa_end": null,
"aa_length": 556,
"cds_start": 61,
"cds_end": null,
"cds_length": 1671,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001770.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000538922.8"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.61G>C",
"hgvs_p": "p.Glu21Gln",
"transcript": "ENST00000324662.8",
"protein_id": "ENSP00000313419.4",
"transcript_support_level": 1,
"aa_start": 21,
"aa_end": null,
"aa_length": 557,
"cds_start": 61,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000324662.8"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.61G>C",
"hgvs_p": "p.Glu21Gln",
"transcript": "NM_001178098.2",
"protein_id": "NP_001171569.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 557,
"cds_start": 61,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001178098.2"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.61G>C",
"hgvs_p": "p.Glu21Gln",
"transcript": "NM_001385732.1",
"protein_id": "NP_001372661.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 467,
"cds_start": 61,
"cds_end": null,
"cds_length": 1404,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001385732.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "c.61G>C",
"hgvs_p": "p.Glu21Gln",
"transcript": "XM_011545981.3",
"protein_id": "XP_011544283.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 282,
"cds_start": 61,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011545981.3"
},
{
"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+4203C>G",
"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": null,
"cds_end": null,
"cds_length": 133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000566762.1"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "n.97G>C",
"hgvs_p": null,
"transcript": "ENST00000565089.5",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000565089.5"
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "n.91G>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_169755.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"hgvs_c": "n.91G>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_950871.3"
}
],
"gene_symbol": "CD19",
"gene_hgnc_id": 1633,
"dbsnp": "rs771929657",
"frequency_reference_population": 6.8408065e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84081e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.030639976263046265,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.052,
"revel_prediction": "Benign",
"alphamissense_score": 0.0844,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.837,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001178098.2",
"gene_symbol": "CD19",
"hgnc_id": 1633,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.61G>C",
"hgvs_p": "p.Glu21Gln"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000566762.1",
"gene_symbol": "RABEP2",
"hgnc_id": 24817,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-150+4203C>G",
"hgvs_p": null
}
],
"clinvar_disease": " 3, common variable,Immunodeficiency,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Immunodeficiency, common variable, 3|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}