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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: 12-111655618-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=111655618&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 111655618,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_006768.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"hgvs_c": "c.1259G>T",
"hgvs_p": "p.Arg420Leu",
"transcript": "NM_006768.5",
"protein_id": "NP_006759.3",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 592,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1423,
"cdna_end": null,
"cdna_length": 3996,
"mane_select": "ENST00000419234.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"hgvs_c": "c.1259G>T",
"hgvs_p": "p.Arg420Leu",
"transcript": "ENST00000419234.9",
"protein_id": "ENSP00000403524.3",
"transcript_support_level": 1,
"aa_start": 420,
"aa_end": null,
"aa_length": 592,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1423,
"cdna_end": null,
"cdna_length": 3996,
"mane_select": "NM_006768.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"hgvs_c": "c.1169G>T",
"hgvs_p": "p.Arg390Leu",
"transcript": "ENST00000327551.6",
"protein_id": "ENSP00000330813.5",
"transcript_support_level": 1,
"aa_start": 390,
"aa_end": null,
"aa_length": 562,
"cds_start": 1169,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 1310,
"cdna_end": null,
"cdna_length": 1947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"hgvs_c": "c.1382G>T",
"hgvs_p": "p.Arg461Leu",
"transcript": "XM_005253944.5",
"protein_id": "XP_005254001.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 633,
"cds_start": 1382,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 1546,
"cdna_end": null,
"cdna_length": 4119,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"hgvs_c": "c.1097G>T",
"hgvs_p": "p.Arg366Leu",
"transcript": "XM_017019992.2",
"protein_id": "XP_016875481.1",
"transcript_support_level": null,
"aa_start": 366,
"aa_end": null,
"aa_length": 538,
"cds_start": 1097,
"cds_end": null,
"cds_length": 1617,
"cdna_start": 1261,
"cdna_end": null,
"cdna_length": 3834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"hgvs_c": "c.812G>T",
"hgvs_p": "p.Arg271Leu",
"transcript": "XM_047429622.1",
"protein_id": "XP_047285578.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 443,
"cds_start": 812,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 3453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"hgvs_c": "c.398G>T",
"hgvs_p": "p.Arg133Leu",
"transcript": "XM_047429623.1",
"protein_id": "XP_047285579.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 305,
"cds_start": 398,
"cds_end": null,
"cds_length": 918,
"cdna_start": 477,
"cdna_end": null,
"cdna_length": 3050,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"hgvs_c": "n.1163G>T",
"hgvs_p": null,
"transcript": "ENST00000547043.1",
"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": 1543,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BRAP",
"gene_hgnc_id": 1099,
"dbsnp": "rs746619992",
"frequency_reference_population": 6.842791e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84279e-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": 0.8923548460006714,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.7,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9913,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"phylop100way_prediction": "Pathogenic",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006768.5",
"gene_symbol": "BRAP",
"hgnc_id": 1099,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1259G>T",
"hgvs_p": "p.Arg420Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}