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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: 3-33114165-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=33114165&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 33114165,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006371.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "NM_006371.5",
"protein_id": "NP_006362.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 401,
"cds_start": 88,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000320954.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006371.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "ENST00000320954.11",
"protein_id": "ENSP00000323696.5",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 401,
"cds_start": 88,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006371.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000320954.11"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "ENST00000946650.1",
"protein_id": "ENSP00000616709.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 412,
"cds_start": 88,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946650.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "ENST00000946648.1",
"protein_id": "ENSP00000616707.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 400,
"cds_start": 88,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946648.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "ENST00000946649.1",
"protein_id": "ENSP00000616708.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 397,
"cds_start": 88,
"cds_end": null,
"cds_length": 1194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946649.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "ENST00000946647.1",
"protein_id": "ENSP00000616706.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 374,
"cds_start": 88,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946647.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "NM_001393363.1",
"protein_id": "NP_001380292.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 373,
"cds_start": 88,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393363.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "ENST00000858647.1",
"protein_id": "ENSP00000528706.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 373,
"cds_start": 88,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858647.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "NM_001393364.1",
"protein_id": "NP_001380293.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 358,
"cds_start": 88,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393364.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "ENST00000449224.1",
"protein_id": "ENSP00000409997.1",
"transcript_support_level": 2,
"aa_start": 30,
"aa_end": null,
"aa_length": 358,
"cds_start": 88,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449224.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "NM_001393365.1",
"protein_id": "NP_001380294.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 351,
"cds_start": 88,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393365.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys",
"transcript": "ENST00000858648.1",
"protein_id": "ENSP00000528707.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 351,
"cds_start": 88,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858648.1"
}
],
"gene_symbol": "CRTAP",
"gene_hgnc_id": 2379,
"dbsnp": "rs553076085",
"frequency_reference_population": 0.000048462665,
"hom_count_reference_population": 2,
"allele_count_reference_population": 77,
"gnomad_exomes_af": 0.0000473317,
"gnomad_genomes_af": 0.0000591389,
"gnomad_exomes_ac": 68,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3571507930755615,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.445,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5788,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.222,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_006371.5",
"gene_symbol": "CRTAP",
"hgnc_id": 2379,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Cys"
}
],
"clinvar_disease": "Osteogenesis imperfecta type 7",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Osteogenesis imperfecta type 7",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}