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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: 17-4819490-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4819490&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 4819490,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000263088.11",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2370G>T",
"hgvs_p": "p.Leu790Leu",
"transcript": "NM_002663.5",
"protein_id": "NP_002654.3",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 933,
"cds_start": 2370,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2445,
"cdna_end": null,
"cdna_length": 3443,
"mane_select": "ENST00000263088.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2370G>T",
"hgvs_p": "p.Leu790Leu",
"transcript": "ENST00000263088.11",
"protein_id": "ENSP00000263088.5",
"transcript_support_level": 1,
"aa_start": 790,
"aa_end": null,
"aa_length": 933,
"cds_start": 2370,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2445,
"cdna_end": null,
"cdna_length": 3443,
"mane_select": "NM_002663.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2370G>T",
"hgvs_p": "p.Leu790Leu",
"transcript": "ENST00000572940.5",
"protein_id": "ENSP00000459571.1",
"transcript_support_level": 1,
"aa_start": 790,
"aa_end": null,
"aa_length": 922,
"cds_start": 2370,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 2428,
"cdna_end": null,
"cdna_length": 3391,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2370G>T",
"hgvs_p": "p.Leu790Leu",
"transcript": "NM_001243108.2",
"protein_id": "NP_001230037.1",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 922,
"cds_start": 2370,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 2445,
"cdna_end": null,
"cdna_length": 3410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.261G>T",
"hgvs_p": "p.Leu87Leu",
"transcript": "ENST00000576864.1",
"protein_id": "ENSP00000460477.1",
"transcript_support_level": 3,
"aa_start": 87,
"aa_end": null,
"aa_length": 196,
"cds_start": 261,
"cds_end": null,
"cds_length": 591,
"cdna_start": 262,
"cdna_end": null,
"cdna_length": 726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.564G>T",
"hgvs_p": "p.Leu188Leu",
"transcript": "ENST00000576983.5",
"protein_id": "ENSP00000460250.2",
"transcript_support_level": 3,
"aa_start": 188,
"aa_end": null,
"aa_length": 195,
"cds_start": 564,
"cds_end": null,
"cds_length": 589,
"cdna_start": 564,
"cdna_end": null,
"cdna_length": 589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2010G>T",
"hgvs_p": "p.Leu670Leu",
"transcript": "XM_047436300.1",
"protein_id": "XP_047292256.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 813,
"cds_start": 2010,
"cds_end": null,
"cds_length": 2442,
"cdna_start": 2200,
"cdna_end": null,
"cdna_length": 3198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "n.*25G>T",
"hgvs_p": null,
"transcript": "ENST00000572127.1",
"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": 632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"dbsnp": "rs1052751",
"frequency_reference_population": 6.841199e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8412e-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": -0.4300000071525574,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.549,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP7",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000263088.11",
"gene_symbol": "PLD2",
"hgnc_id": 9068,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2370G>T",
"hgvs_p": "p.Leu790Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}