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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: 1-150750072-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=150750072&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 150750072,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004079.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Ala243Thr",
"transcript": "NM_004079.5",
"protein_id": "NP_004070.3",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 331,
"cds_start": 727,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000368985.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004079.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Ala243Thr",
"transcript": "ENST00000368985.8",
"protein_id": "ENSP00000357981.3",
"transcript_support_level": 1,
"aa_start": 243,
"aa_end": null,
"aa_length": 331,
"cds_start": 727,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004079.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368985.8"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Ala243Thr",
"transcript": "ENST00000857596.1",
"protein_id": "ENSP00000527655.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 331,
"cds_start": 727,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857596.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Ala243Thr",
"transcript": "ENST00000962999.1",
"protein_id": "ENSP00000633058.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 330,
"cds_start": 727,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962999.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "ENST00000857595.1",
"protein_id": "ENSP00000527654.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 329,
"cds_start": 721,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857595.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Ala243Thr",
"transcript": "ENST00000679512.1",
"protein_id": "ENSP00000505113.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 309,
"cds_start": 727,
"cds_end": null,
"cds_length": 930,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679512.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.577G>A",
"hgvs_p": "p.Ala193Thr",
"transcript": "NM_001199739.2",
"protein_id": "NP_001186668.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 281,
"cds_start": 577,
"cds_end": null,
"cds_length": 846,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199739.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.577G>A",
"hgvs_p": "p.Ala193Thr",
"transcript": "ENST00000680288.1",
"protein_id": "ENSP00000506001.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 281,
"cds_start": 577,
"cds_end": null,
"cds_length": 846,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680288.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.577G>A",
"hgvs_p": "p.Ala193Thr",
"transcript": "ENST00000963000.1",
"protein_id": "ENSP00000633059.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 280,
"cds_start": 577,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963000.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.550G>A",
"hgvs_p": "p.Ala184Thr",
"transcript": "ENST00000680664.1",
"protein_id": "ENSP00000506248.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 272,
"cds_start": 550,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680664.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Ala243Thr",
"transcript": "ENST00000681728.1",
"protein_id": "ENSP00000505313.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 267,
"cds_start": 727,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000681728.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.499G>A",
"hgvs_p": "p.Ala167Thr",
"transcript": "ENST00000448301.7",
"protein_id": "ENSP00000408414.2",
"transcript_support_level": 2,
"aa_start": 167,
"aa_end": null,
"aa_length": 255,
"cds_start": 499,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000448301.7"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.454G>A",
"hgvs_p": "p.Ala152Thr",
"transcript": "ENST00000679898.1",
"protein_id": "ENSP00000505326.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 240,
"cds_start": 454,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679898.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "c.627+1709G>A",
"hgvs_p": null,
"transcript": "ENST00000680311.1",
"protein_id": "ENSP00000505020.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 215,
"cds_start": null,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680311.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "n.727G>A",
"hgvs_p": null,
"transcript": "ENST00000472977.7",
"protein_id": "ENSP00000475176.2",
"transcript_support_level": 5,
"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": "ENST00000472977.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "n.727G>A",
"hgvs_p": null,
"transcript": "ENST00000483930.2",
"protein_id": "ENSP00000475812.2",
"transcript_support_level": 5,
"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": "ENST00000483930.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "n.727G>A",
"hgvs_p": null,
"transcript": "ENST00000607427.2",
"protein_id": "ENSP00000475557.2",
"transcript_support_level": 2,
"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": "ENST00000607427.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "n.727G>A",
"hgvs_p": null,
"transcript": "ENST00000680931.1",
"protein_id": "ENSP00000504934.1",
"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": "ENST00000680931.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "n.727G>A",
"hgvs_p": null,
"transcript": "ENST00000681444.1",
"protein_id": "ENSP00000505359.1",
"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": "ENST00000681444.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"hgvs_c": "n.627+1709G>A",
"hgvs_p": null,
"transcript": "ENST00000680471.1",
"protein_id": "ENSP00000506603.1",
"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": "ENST00000680471.1"
}
],
"gene_symbol": "CTSS",
"gene_hgnc_id": 2545,
"dbsnp": "rs748861303",
"frequency_reference_population": 0.000004788833,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000478883,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9226375818252563,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.73,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3227,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.947,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004079.5",
"gene_symbol": "CTSS",
"hgnc_id": 2545,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Ala243Thr"
}
],
"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
}