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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: 1-235663082-TAA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=235663082&ref=TAA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 235663082,
"ref": "TAA",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000389793.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": 52,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.11268-6_11268-5delTT",
"hgvs_p": null,
"transcript": "NM_000081.4",
"protein_id": "NP_000072.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3801,
"cds_start": -4,
"cds_end": null,
"cds_length": 11406,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13466,
"mane_select": "ENST00000389793.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": 52,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.11268-6_11268-5delTT",
"hgvs_p": null,
"transcript": "ENST00000389793.7",
"protein_id": "ENSP00000374443.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 3801,
"cds_start": -4,
"cds_end": null,
"cds_length": 11406,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13466,
"mane_select": "NM_000081.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": 52,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.11268-6_11268-5delTT",
"hgvs_p": null,
"transcript": "NM_001301365.1",
"protein_id": "NP_001288294.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3801,
"cds_start": -4,
"cds_end": null,
"cds_length": 11406,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1818-6_1818-5delTT",
"hgvs_p": null,
"transcript": "ENST00000697235.1",
"protein_id": "ENSP00000513202.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 651,
"cds_start": -4,
"cds_end": null,
"cds_length": 1956,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.3087-6_3087-5delTT",
"hgvs_p": null,
"transcript": "ENST00000462376.2",
"protein_id": null,
"transcript_support_level": 4,
"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": 5087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.6258-6_6258-5delTT",
"hgvs_p": null,
"transcript": "ENST00000473037.5",
"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": 8293,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": 51,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.*7254-6_*7254-5delTT",
"hgvs_p": null,
"transcript": "ENST00000697178.1",
"protein_id": "ENSP00000513163.1",
"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": 13920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.*1696-6_*1696-5delTT",
"hgvs_p": null,
"transcript": "ENST00000697236.1",
"protein_id": "ENSP00000513203.1",
"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": 6723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.*1225-6_*1225-5delTT",
"hgvs_p": null,
"transcript": "ENST00000697237.1",
"protein_id": "ENSP00000513204.1",
"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": 3918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.422-6_422-5delTT",
"hgvs_p": null,
"transcript": "ENST00000697238.1",
"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": 1035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.662-6_662-5delTT",
"hgvs_p": null,
"transcript": "ENST00000697239.1",
"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": 1275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.*104-6_*104-5delTT",
"hgvs_p": null,
"transcript": "ENST00000697240.1",
"protein_id": "ENSP00000513205.1",
"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": 3784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": 53,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.11430-6_11430-5delTT",
"hgvs_p": null,
"transcript": "XM_011544031.2",
"protein_id": "XP_011542333.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3855,
"cds_start": -4,
"cds_end": null,
"cds_length": 11568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": 53,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.11430-6_11430-5delTT",
"hgvs_p": null,
"transcript": "XM_011544032.2",
"protein_id": "XP_011542334.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3855,
"cds_start": -4,
"cds_end": null,
"cds_length": 11568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 14101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": 53,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.11430-6_11430-5delTT",
"hgvs_p": null,
"transcript": "XM_011544033.3",
"protein_id": "XP_011542335.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3855,
"cds_start": -4,
"cds_end": null,
"cds_length": 11568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 15425,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": 53,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.11430-6_11430-5delTT",
"hgvs_p": null,
"transcript": "XM_047443026.1",
"protein_id": "XP_047298982.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3855,
"cds_start": -4,
"cds_end": null,
"cds_length": 11568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 20517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": 49,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.9093-6_9093-5delTT",
"hgvs_p": null,
"transcript": "XM_011544036.3",
"protein_id": "XP_011542338.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3076,
"cds_start": -4,
"cds_end": null,
"cds_length": 9231,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 48,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.8931-6_8931-5delTT",
"hgvs_p": null,
"transcript": "XM_047443034.1",
"protein_id": "XP_047298990.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3022,
"cds_start": -4,
"cds_end": null,
"cds_length": 9069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"dbsnp": "rs36014994",
"frequency_reference_population": 0.0110348705,
"hom_count_reference_population": 22,
"allele_count_reference_population": 14506,
"gnomad_exomes_af": 0.0117426,
"gnomad_genomes_af": 0.00551539,
"gnomad_exomes_ac": 13682,
"gnomad_genomes_ac": 824,
"gnomad_exomes_homalt": 8,
"gnomad_genomes_homalt": 14,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.138,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000389793.7",
"gene_symbol": "LYST",
"hgnc_id": 1968,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.11268-6_11268-5delTT",
"hgvs_p": null
}
],
"clinvar_disease": "Chédiak-Higashi syndrome,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Chédiak-Higashi syndrome|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}