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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: X-75424763-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=75424763&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 75424763,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_144969.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.625T>C",
"hgvs_p": "p.Ser209Pro",
"transcript": "NM_144969.3",
"protein_id": "NP_659406.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 337,
"cds_start": 625,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 5578,
"mane_select": "ENST00000373367.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.625T>C",
"hgvs_p": "p.Ser209Pro",
"transcript": "ENST00000373367.8",
"protein_id": "ENSP00000362465.3",
"transcript_support_level": 1,
"aa_start": 209,
"aa_end": null,
"aa_length": 337,
"cds_start": 625,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 5578,
"mane_select": "NM_144969.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.598T>C",
"hgvs_p": "p.Ser200Pro",
"transcript": "NM_001146256.2",
"protein_id": "NP_001139728.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 328,
"cds_start": 598,
"cds_end": null,
"cds_length": 987,
"cdna_start": 611,
"cdna_end": null,
"cdna_length": 5551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.598T>C",
"hgvs_p": "p.Ser200Pro",
"transcript": "ENST00000541184.1",
"protein_id": "ENSP00000445420.1",
"transcript_support_level": 2,
"aa_start": 200,
"aa_end": null,
"aa_length": 328,
"cds_start": 598,
"cds_end": null,
"cds_length": 987,
"cdna_start": 1076,
"cdna_end": null,
"cdna_length": 6012,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.625T>C",
"hgvs_p": "p.Ser209Pro",
"transcript": "XM_006724624.5",
"protein_id": "XP_006724687.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 337,
"cds_start": 625,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 2059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.625T>C",
"hgvs_p": "p.Ser209Pro",
"transcript": "XM_047441865.1",
"protein_id": "XP_047297821.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 337,
"cds_start": 625,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 3232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.625T>C",
"hgvs_p": "p.Ser209Pro",
"transcript": "XM_017029296.3",
"protein_id": "XP_016884785.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 328,
"cds_start": 625,
"cds_end": null,
"cds_length": 987,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 1198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.598T>C",
"hgvs_p": "p.Ser200Pro",
"transcript": "XM_047441866.1",
"protein_id": "XP_047297822.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 328,
"cds_start": 598,
"cds_end": null,
"cds_length": 987,
"cdna_start": 611,
"cdna_end": null,
"cdna_length": 3205,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.598T>C",
"hgvs_p": "p.Ser200Pro",
"transcript": "XM_047441867.1",
"protein_id": "XP_047297823.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 328,
"cds_start": 598,
"cds_end": null,
"cds_length": 987,
"cdna_start": 611,
"cdna_end": null,
"cdna_length": 2032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.598T>C",
"hgvs_p": "p.Ser200Pro",
"transcript": "XM_047441868.1",
"protein_id": "XP_047297824.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 319,
"cds_start": 598,
"cds_end": null,
"cds_length": 960,
"cdna_start": 611,
"cdna_end": null,
"cdna_length": 1171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.301T>C",
"hgvs_p": "p.Ser101Pro",
"transcript": "XM_024452342.1",
"protein_id": "XP_024308110.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 229,
"cds_start": 301,
"cds_end": null,
"cds_length": 690,
"cdna_start": 1202,
"cdna_end": null,
"cdna_length": 6142,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "c.178T>C",
"hgvs_p": "p.Ser60Pro",
"transcript": "XM_047441869.1",
"protein_id": "XP_047297825.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 188,
"cds_start": 178,
"cds_end": null,
"cds_length": 567,
"cdna_start": 1081,
"cdna_end": null,
"cdna_length": 3675,
"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": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "n.638T>C",
"hgvs_p": null,
"transcript": "XR_001755658.3",
"protein_id": null,
"transcript_support_level": null,
"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": 5646,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "n.517T>C",
"hgvs_p": null,
"transcript": "XR_007068181.1",
"protein_id": null,
"transcript_support_level": null,
"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": 712,
"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": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"hgvs_c": "n.638T>C",
"hgvs_p": null,
"transcript": "XR_938393.3",
"protein_id": null,
"transcript_support_level": null,
"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": 6819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZDHHC15",
"gene_hgnc_id": 20342,
"dbsnp": "rs1470113586",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.561108410358429,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.156,
"revel_prediction": "Benign",
"alphamissense_score": 0.3541,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.172,
"phylop100way_prediction": "Uncertain_significance",
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_144969.3",
"gene_symbol": "ZDHHC15",
"hgnc_id": 20342,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,Unknown",
"hgvs_c": "c.625T>C",
"hgvs_p": "p.Ser209Pro"
}
],
"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
}