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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: 1-150806780-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=150806780&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 150806780,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000271651.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro",
"transcript": "NM_000396.4",
"protein_id": "NP_000387.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 329,
"cds_start": 26,
"cds_end": null,
"cds_length": 990,
"cdna_start": 74,
"cdna_end": null,
"cdna_length": 1629,
"mane_select": "ENST00000271651.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro",
"transcript": "ENST00000271651.8",
"protein_id": "ENSP00000271651.3",
"transcript_support_level": 1,
"aa_start": 9,
"aa_end": null,
"aa_length": 329,
"cds_start": 26,
"cds_end": null,
"cds_length": 990,
"cdna_start": 74,
"cdna_end": null,
"cdna_length": 1629,
"mane_select": "NM_000396.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.203T>C",
"hgvs_p": "p.Leu68Pro",
"transcript": "ENST00000443913.2",
"protein_id": "ENSP00000405083.2",
"transcript_support_level": 3,
"aa_start": 68,
"aa_end": null,
"aa_length": 388,
"cds_start": 203,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 213,
"cdna_end": null,
"cdna_length": 1768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.68T>C",
"hgvs_p": "p.Leu23Pro",
"transcript": "ENST00000677887.1",
"protein_id": "ENSP00000503876.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 343,
"cds_start": 68,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 167,
"cdna_end": null,
"cdna_length": 1722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.62T>C",
"hgvs_p": "p.Leu21Pro",
"transcript": "ENST00000678337.1",
"protein_id": "ENSP00000504759.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 341,
"cds_start": 62,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 782,
"cdna_end": null,
"cdna_length": 3665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro",
"transcript": "ENST00000676970.1",
"protein_id": "ENSP00000503832.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 333,
"cds_start": 26,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 74,
"cdna_end": null,
"cdna_length": 1641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro",
"transcript": "ENST00000676751.1",
"protein_id": "ENSP00000502964.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 330,
"cds_start": 26,
"cds_end": null,
"cds_length": 993,
"cdna_start": 74,
"cdna_end": null,
"cdna_length": 1523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro",
"transcript": "ENST00000676824.1",
"protein_id": "ENSP00000504176.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 329,
"cds_start": 26,
"cds_end": null,
"cds_length": 990,
"cdna_start": 340,
"cdna_end": null,
"cdna_length": 1895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro",
"transcript": "ENST00000676966.1",
"protein_id": "ENSP00000503723.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 329,
"cds_start": 26,
"cds_end": null,
"cds_length": 990,
"cdna_start": 165,
"cdna_end": null,
"cdna_length": 1720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro",
"transcript": "ENST00000676716.1",
"protein_id": "ENSP00000504737.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 288,
"cds_start": 26,
"cds_end": null,
"cds_length": 867,
"cdna_start": 27,
"cdna_end": null,
"cdna_length": 1459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro",
"transcript": "ENST00000679260.1",
"protein_id": "ENSP00000504534.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 256,
"cds_start": 26,
"cds_end": null,
"cds_length": 771,
"cdna_start": 74,
"cdna_end": null,
"cdna_length": 1410,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.2634T>C",
"hgvs_p": null,
"transcript": "ENST00000480670.2",
"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": 4619,
"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": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.26T>C",
"hgvs_p": null,
"transcript": "ENST00000676680.1",
"protein_id": "ENSP00000503270.1",
"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": 1625,
"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": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.1391T>C",
"hgvs_p": null,
"transcript": "ENST00000677330.1",
"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": 3358,
"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": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.26T>C",
"hgvs_p": null,
"transcript": "ENST00000678275.1",
"protein_id": "ENSP00000504796.1",
"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": 1712,
"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": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.1003T>C",
"hgvs_p": null,
"transcript": "ENST00000678725.1",
"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": 2808,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.150T>C",
"hgvs_p": null,
"transcript": "ENST00000679090.1",
"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": 2398,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.906T>C",
"hgvs_p": null,
"transcript": "ENST00000679148.1",
"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": 4522,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"hgvs_c": "n.1926T>C",
"hgvs_p": null,
"transcript": "ENST00000679171.1",
"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": 4001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CTSK",
"gene_hgnc_id": 2536,
"dbsnp": "rs1057517252",
"frequency_reference_population": 0.0000027363226,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273632,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9630042314529419,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.776,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2937,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.339,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000271651.8",
"gene_symbol": "CTSK",
"hgnc_id": 2536,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.26T>C",
"hgvs_p": "p.Leu9Pro"
}
],
"clinvar_disease": "Pyknodysostosis,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:4",
"phenotype_combined": "Pyknodysostosis|not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}