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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: 2-204546016-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=204546016&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 204546016,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001302769.2",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr",
"transcript": "NM_001302769.2",
"protein_id": "NP_001289698.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1205,
"cds_start": 17,
"cds_end": null,
"cds_length": 3618,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 8492,
"mane_select": "ENST00000406610.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr",
"transcript": "ENST00000406610.7",
"protein_id": "ENSP00000385848.2",
"transcript_support_level": 1,
"aa_start": 6,
"aa_end": null,
"aa_length": 1205,
"cds_start": 17,
"cds_end": null,
"cds_length": 3618,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 8492,
"mane_select": "NM_001302769.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr",
"transcript": "ENST00000358768.6",
"protein_id": "ENSP00000351618.2",
"transcript_support_level": 1,
"aa_start": 6,
"aa_end": null,
"aa_length": 1143,
"cds_start": 17,
"cds_end": null,
"cds_length": 3432,
"cdna_start": 17,
"cdna_end": null,
"cdna_length": 3432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr",
"transcript": "ENST00000351153.5",
"protein_id": "ENSP00000317261.2",
"transcript_support_level": 1,
"aa_start": 6,
"aa_end": null,
"aa_length": 1136,
"cds_start": 17,
"cds_end": null,
"cds_length": 3411,
"cdna_start": 17,
"cdna_end": null,
"cdna_length": 3411,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr",
"transcript": "ENST00000349953.7",
"protein_id": "ENSP00000340280.3",
"transcript_support_level": 1,
"aa_start": 6,
"aa_end": null,
"aa_length": 1104,
"cds_start": 17,
"cds_end": null,
"cds_length": 3315,
"cdna_start": 17,
"cdna_end": null,
"cdna_length": 3315,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "n.17G>A",
"hgvs_p": null,
"transcript": "ENST00000415947.1",
"protein_id": "ENSP00000407718.1",
"transcript_support_level": 1,
"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": 1668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr",
"transcript": "NM_152526.6",
"protein_id": "NP_689739.4",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1143,
"cds_start": 17,
"cds_end": null,
"cds_length": 3432,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 8306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr",
"transcript": "NM_057177.7",
"protein_id": "NP_476518.4",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1136,
"cds_start": 17,
"cds_end": null,
"cds_length": 3411,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 8285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr",
"transcript": "NM_205863.4",
"protein_id": "NP_995585.2",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1104,
"cds_start": 17,
"cds_end": null,
"cds_length": 3315,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 8189,
"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": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "n.175G>A",
"hgvs_p": null,
"transcript": "ENST00000471958.1",
"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": 441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"hgvs_c": "c.-5297G>A",
"hgvs_p": null,
"transcript": "XM_047443208.1",
"protein_id": "XP_047299164.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1213,
"cds_start": -4,
"cds_end": null,
"cds_length": 3642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PARD3B",
"gene_hgnc_id": 14446,
"dbsnp": "rs980990963",
"frequency_reference_population": 0.00001275385,
"hom_count_reference_population": 1,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.00000776853,
"gnomad_genomes_af": 0.0000591389,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7891706228256226,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.315,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3173,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.007,
"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": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001302769.2",
"gene_symbol": "PARD3B",
"hgnc_id": 14446,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.17G>A",
"hgvs_p": "p.Cys6Tyr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}