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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: 13-24913007-AG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=24913007&ref=AG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 24913007,
"ref": "AG",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000381884.9",
"consequences": [
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs",
"transcript": "NM_018451.5",
"protein_id": "NP_060921.3",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1338,
"cds_start": 18,
"cds_end": null,
"cds_length": 4017,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 5082,
"mane_select": "ENST00000381884.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPJ",
"gene_hgnc_id": 17272,
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs",
"transcript": "ENST00000381884.9",
"protein_id": "ENSP00000371308.4",
"transcript_support_level": 1,
"aa_start": 6,
"aa_end": null,
"aa_length": 1338,
"cds_start": 18,
"cds_end": null,
"cds_length": 4017,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 5082,
"mane_select": "NM_018451.5",
"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": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPJ",
"gene_hgnc_id": 17272,
"hgvs_c": "n.18delC",
"hgvs_p": null,
"transcript": "ENST00000616936.4",
"protein_id": "ENSP00000477511.1",
"transcript_support_level": 1,
"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": 5020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs",
"transcript": "XM_047430483.1",
"protein_id": "XP_047286439.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1338,
"cds_start": 18,
"cds_end": null,
"cds_length": 4017,
"cdna_start": 689,
"cdna_end": null,
"cdna_length": 5586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs",
"transcript": "XM_011535149.3",
"protein_id": "XP_011533451.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1136,
"cds_start": 18,
"cds_end": null,
"cds_length": 3411,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 3685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs",
"transcript": "XM_047430484.1",
"protein_id": "XP_047286440.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1136,
"cds_start": 18,
"cds_end": null,
"cds_length": 3411,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 4154,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs",
"transcript": "XM_011535150.3",
"protein_id": "XP_011533452.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1129,
"cds_start": 18,
"cds_end": null,
"cds_length": 3390,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 5387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs",
"transcript": "XM_017020673.2",
"protein_id": "XP_016876162.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 1015,
"cds_start": 18,
"cds_end": null,
"cds_length": 3048,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 3299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs",
"transcript": "XM_047430485.1",
"protein_id": "XP_047286441.1",
"transcript_support_level": null,
"aa_start": 6,
"aa_end": null,
"aa_length": 999,
"cds_start": 18,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 3203,
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPJ",
"gene_hgnc_id": 17272,
"hgvs_c": "n.18delC",
"hgvs_p": null,
"transcript": "ENST00000545981.6",
"protein_id": "ENSP00000441090.2",
"transcript_support_level": 2,
"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": 4298,
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "n.185delC",
"hgvs_p": null,
"transcript": "NR_047594.2",
"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": 5199,
"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": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "n.185delC",
"hgvs_p": null,
"transcript": "NR_047595.2",
"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": 4997,
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "n.185delC",
"hgvs_p": null,
"transcript": "XR_941627.2",
"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": 3824,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPAP",
"gene_hgnc_id": 17272,
"hgvs_c": "n.185delC",
"hgvs_p": null,
"transcript": "XR_941628.2",
"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": 3422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CENPJ",
"gene_hgnc_id": 17272,
"dbsnp": "rs199422202",
"frequency_reference_population": 0.000002736491,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273649,
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.625,
"phylop100way_prediction": "Benign",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000381884.9",
"gene_symbol": "CENPJ",
"hgnc_id": 17272,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs"
},
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_018451.5",
"gene_symbol": "CPAP",
"hgnc_id": 17272,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.18delC",
"hgvs_p": "p.Ser7fs"
}
],
"clinvar_disease": " autosomal recessive, primary,Microcephaly 1,Microcephaly 6,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 O:1",
"phenotype_combined": "Microcephaly 6, primary, autosomal recessive|Microcephaly 1, primary, autosomal recessive|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}