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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: 13-52455635-CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=52455635&ref=CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 52455635,
"ref": "CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG",
"alt": "C",
"effect": "intron_variant",
"transcript": "NM_001098525.3",
"consequences": [
{
"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": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG",
"hgvs_p": null,
"transcript": "NM_018204.5",
"protein_id": "NP_060674.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 682,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG",
"hgvs_p": null,
"transcript": "ENST00000258607.10",
"protein_id": "ENSP00000258607.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 682,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG",
"hgvs_p": null,
"transcript": "ENST00000378037.9",
"protein_id": "ENSP00000367276.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 683,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG",
"hgvs_p": null,
"transcript": "ENST00000378034.7",
"protein_id": "ENSP00000367273.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 494,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG",
"hgvs_p": null,
"transcript": "NM_001098525.3",
"protein_id": "NP_001091995.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 683,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG",
"hgvs_p": null,
"transcript": "ENST00000898697.1",
"protein_id": "ENSP00000568756.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 669,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG",
"hgvs_p": null,
"transcript": "ENST00000898699.1",
"protein_id": "ENSP00000568758.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 668,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG",
"hgvs_p": null,
"transcript": "NM_001286687.2",
"protein_id": "NP_001273616.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 494,
"cds_start": null,
"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": 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": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG",
"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"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"hgvs_c": "c.-101+10_-101+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG",
"hgvs_p": null,
"transcript": "ENST00000468284.1",
"protein_id": "ENSP00000418431.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 92,
"cds_start": null,
"cds_end": null,
"cds_length": 281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000468284.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CKAP2-DT",
"gene_hgnc_id": 56053,
"hgvs_c": "n.-262_-233delCACCGCCACCGCCACCGCCACCGCCACCGC",
"hgvs_p": null,
"transcript": "ENST00000614364.3",
"protein_id": null,
"transcript_support_level": 6,
"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": "pseudogene",
"feature": "ENST00000614364.3"
}
],
"gene_symbol": "CKAP2",
"gene_hgnc_id": 1990,
"dbsnp": "rs72440971",
"frequency_reference_population": 0.0009468073,
"hom_count_reference_population": 5,
"allele_count_reference_population": 1480,
"gnomad_exomes_af": 0.000958672,
"gnomad_genomes_af": 0.000836517,
"gnomad_exomes_ac": 1353,
"gnomad_genomes_ac": 127,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 3.629,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"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": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001098525.3",
"gene_symbol": "CKAP2",
"hgnc_id": 1990,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000614364.3",
"gene_symbol": "CKAP2-DT",
"hgnc_id": 56053,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-262_-233delCACCGCCACCGCCACCGCCACCGCCACCGC",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}