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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: 13-52461604-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=52461604&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 52461604,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001098525.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.778C>T",
"hgvs_p": "p.His260Tyr",
"transcript": "NM_018204.5",
"protein_id": "NP_060674.3",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 682,
"cds_start": 778,
"cds_end": null,
"cds_length": 2049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000258607.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018204.5"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.778C>T",
"hgvs_p": "p.His260Tyr",
"transcript": "ENST00000258607.10",
"protein_id": "ENSP00000258607.5",
"transcript_support_level": 1,
"aa_start": 260,
"aa_end": null,
"aa_length": 682,
"cds_start": 778,
"cds_end": null,
"cds_length": 2049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018204.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258607.10"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.781C>T",
"hgvs_p": "p.His261Tyr",
"transcript": "ENST00000378037.9",
"protein_id": "ENSP00000367276.4",
"transcript_support_level": 1,
"aa_start": 261,
"aa_end": null,
"aa_length": 683,
"cds_start": 781,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378037.9"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.778C>T",
"hgvs_p": "p.His260Tyr",
"transcript": "ENST00000378034.7",
"protein_id": "ENSP00000367273.2",
"transcript_support_level": 1,
"aa_start": 260,
"aa_end": null,
"aa_length": 494,
"cds_start": 778,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378034.7"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.781C>T",
"hgvs_p": "p.His261Tyr",
"transcript": "NM_001098525.3",
"protein_id": "NP_001091995.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 683,
"cds_start": 781,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001098525.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.781C>T",
"hgvs_p": "p.His261Tyr",
"transcript": "ENST00000898697.1",
"protein_id": "ENSP00000568756.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 669,
"cds_start": 781,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898697.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.778C>T",
"hgvs_p": "p.His260Tyr",
"transcript": "ENST00000898699.1",
"protein_id": "ENSP00000568758.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 668,
"cds_start": 778,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898699.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.634C>T",
"hgvs_p": "p.His212Tyr",
"transcript": "NM_001286686.2",
"protein_id": "NP_001273615.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 634,
"cds_start": 634,
"cds_end": null,
"cds_length": 1905,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001286686.2"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.634C>T",
"hgvs_p": "p.His212Tyr",
"transcript": "ENST00000490903.5",
"protein_id": "ENSP00000417830.1",
"transcript_support_level": 2,
"aa_start": 212,
"aa_end": null,
"aa_length": 634,
"cds_start": 634,
"cds_end": null,
"cds_length": 1905,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000490903.5"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.778C>T",
"hgvs_p": "p.His260Tyr",
"transcript": "NM_001286687.2",
"protein_id": "NP_001273616.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 494,
"cds_start": 778,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001286687.2"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.637C>T",
"hgvs_p": "p.His213Tyr",
"transcript": "XM_005266344.5",
"protein_id": "XP_005266401.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 635,
"cds_start": 637,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005266344.5"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.532C>T",
"hgvs_p": "p.His178Tyr",
"transcript": "XM_047430268.1",
"protein_id": "XP_047286224.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 600,
"cds_start": 532,
"cds_end": null,
"cds_length": 1803,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430268.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.155+4997C>T",
"hgvs_p": null,
"transcript": "ENST00000898698.1",
"protein_id": "ENSP00000568757.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 133,
"cds_start": null,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898698.1"
}
],
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"dbsnp": "rs144431404",
"frequency_reference_population": 0.00045163312,
"hom_count_reference_population": 4,
"allele_count_reference_population": 729,
"gnomad_exomes_af": 0.000245579,
"gnomad_genomes_af": 0.00242954,
"gnomad_exomes_ac": 359,
"gnomad_genomes_ac": 370,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0035355091094970703,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.0847,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.215,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001098525.3",
"gene_symbol": "CKAP2",
"hgnc_id": 1990,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.781C>T",
"hgvs_p": "p.His261Tyr"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}