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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-15822863-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=15822863&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 15822863,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005089.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.1070T>C",
"hgvs_p": "p.Phe357Ser",
"transcript": "NM_005089.4",
"protein_id": "NP_005080.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 482,
"cds_start": 1070,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000307771.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005089.4"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.1070T>C",
"hgvs_p": "p.Phe357Ser",
"transcript": "ENST00000307771.8",
"protein_id": "ENSP00000303015.7",
"transcript_support_level": 1,
"aa_start": 357,
"aa_end": null,
"aa_length": 482,
"cds_start": 1070,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005089.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307771.8"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.1088T>C",
"hgvs_p": "p.Phe363Ser",
"transcript": "ENST00000964213.1",
"protein_id": "ENSP00000634272.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 488,
"cds_start": 1088,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964213.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.1082T>C",
"hgvs_p": "p.Phe361Ser",
"transcript": "ENST00000964212.1",
"protein_id": "ENSP00000634271.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 486,
"cds_start": 1082,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964212.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.1037T>C",
"hgvs_p": "p.Phe346Ser",
"transcript": "ENST00000936517.1",
"protein_id": "ENSP00000606576.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 471,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936517.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.1031T>C",
"hgvs_p": "p.Phe344Ser",
"transcript": "ENST00000879159.1",
"protein_id": "ENSP00000549218.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 469,
"cds_start": 1031,
"cds_end": null,
"cds_length": 1410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879159.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.992T>C",
"hgvs_p": "p.Phe331Ser",
"transcript": "ENST00000684799.1",
"protein_id": "ENSP00000510773.1",
"transcript_support_level": null,
"aa_start": 331,
"aa_end": null,
"aa_length": 460,
"cds_start": 992,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000684799.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.956T>C",
"hgvs_p": "p.Phe319Ser",
"transcript": "ENST00000936516.1",
"protein_id": "ENSP00000606575.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 444,
"cds_start": 956,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936516.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.1139T>C",
"hgvs_p": "p.Phe380Ser",
"transcript": "XM_011545589.4",
"protein_id": "XP_011543891.3",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 505,
"cds_start": 1139,
"cds_end": null,
"cds_length": 1518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011545589.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "c.204-295T>C",
"hgvs_p": null,
"transcript": "ENST00000936518.1",
"protein_id": "ENSP00000606577.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 95,
"cds_start": null,
"cds_end": null,
"cds_length": 288,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936518.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "n.1070T>C",
"hgvs_p": null,
"transcript": "ENST00000690252.1",
"protein_id": "ENSP00000510140.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000690252.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"hgvs_c": "n.956T>C",
"hgvs_p": null,
"transcript": "ENST00000691502.1",
"protein_id": "ENSP00000509336.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000691502.1"
}
],
"gene_symbol": "ZRSR2",
"gene_hgnc_id": 23019,
"dbsnp": "rs1933144258",
"frequency_reference_population": 0.000004956003,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000455264,
"gnomad_genomes_af": 0.00000889759,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0670972466468811,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.072,
"revel_prediction": "Benign",
"alphamissense_score": 0.0886,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.729,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_005089.4",
"gene_symbol": "ZRSR2",
"hgnc_id": 23019,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1070T>C",
"hgvs_p": "p.Phe357Ser"
}
],
"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
}