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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: 3-130680708-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=130680708&ref=C&alt=T&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": "PIK3R4",
"hgnc_id": 8982,
"hgvs_c": "c.3811G>A",
"hgvs_p": "p.Ala1271Thr",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_014602.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 2,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1051,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.19055163860321045,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1358,
"aa_ref": "A",
"aa_start": 1271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5016,
"cdna_start": 4369,
"cds_end": null,
"cds_length": 4077,
"cds_start": 3811,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_014602.3",
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"hgvs_c": "c.3811G>A",
"hgvs_p": "p.Ala1271Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000356763.8",
"protein_coding": true,
"protein_id": "NP_055417.1",
"strand": false,
"transcript": "NM_014602.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1358,
"aa_ref": "A",
"aa_start": 1271,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5016,
"cdna_start": 4369,
"cds_end": null,
"cds_length": 4077,
"cds_start": 3811,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000356763.8",
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"hgvs_c": "c.3811G>A",
"hgvs_p": "p.Ala1271Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014602.3",
"protein_coding": true,
"protein_id": "ENSP00000349205.3",
"strand": false,
"transcript": "ENST00000356763.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1360,
"aa_ref": "A",
"aa_start": 1273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4994,
"cdna_start": 4350,
"cds_end": null,
"cds_length": 4083,
"cds_start": 3817,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000954554.1",
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"hgvs_c": "c.3817G>A",
"hgvs_p": "p.Ala1273Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624613.1",
"strand": false,
"transcript": "ENST00000954554.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1355,
"aa_ref": "A",
"aa_start": 1268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4970,
"cdna_start": 4336,
"cds_end": null,
"cds_length": 4068,
"cds_start": 3802,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000893860.1",
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"hgvs_c": "c.3802G>A",
"hgvs_p": "p.Ala1268Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563919.1",
"strand": false,
"transcript": "ENST00000893860.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1304,
"aa_ref": "A",
"aa_start": 1217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4854,
"cdna_start": 4207,
"cds_end": null,
"cds_length": 3915,
"cds_start": 3649,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000893859.1",
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"hgvs_c": "c.3649G>A",
"hgvs_p": "p.Ala1217Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563918.1",
"strand": false,
"transcript": "ENST00000893859.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 680,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000511760.1",
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"hgvs_c": "n.109G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000511760.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 728,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000512362.5",
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"hgvs_c": "n.541G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000512362.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 744,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000512677.1",
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"hgvs_c": "n.640G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000512677.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs867895592",
"effect": "missense_variant",
"frequency_reference_population": 0.0000013747764,
"gene_hgnc_id": 8982,
"gene_symbol": "PIK3R4",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000137478,
"gnomad_exomes_homalt": 0,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.449,
"pos": 130680708,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.134,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_014602.3"
}
]
}