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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: 12-7088721-GCACTTGATGA-TGTCC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=7088721&ref=GCACTTGATGA&alt=TGTCC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 7088721,
"ref": "GCACTTGATGA",
"alt": "TGTCC",
"effect": "missense_variant,disruptive_inframe_deletion,splice_region_variant",
"transcript": "ENST00000647956.2",
"consequences": [
{
"aa_ref": "IIKC",
"aa_alt": "RT",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"disruptive_inframe_deletion",
"splice_region_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"hgvs_c": "c.917_927delTCATCAAGTGCinsGGACA",
"hgvs_p": "p.Ile306_Cys309delinsArgThr",
"transcript": "NM_001733.7",
"protein_id": "NP_001724.4",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 705,
"cds_start": 917,
"cds_end": null,
"cds_length": 2118,
"cdna_start": 984,
"cdna_end": null,
"cdna_length": 2488,
"mane_select": "ENST00000647956.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "IIKC",
"aa_alt": "RT",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"disruptive_inframe_deletion",
"splice_region_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"hgvs_c": "c.917_927delTCATCAAGTGCinsGGACA",
"hgvs_p": "p.Ile306_Cys309delinsArgThr",
"transcript": "ENST00000647956.2",
"protein_id": "ENSP00000497341.1",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 705,
"cds_start": 917,
"cds_end": null,
"cds_length": 2118,
"cdna_start": 984,
"cdna_end": null,
"cdna_length": 2488,
"mane_select": "NM_001733.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "IIKC",
"aa_alt": "RT",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"disruptive_inframe_deletion",
"splice_region_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"hgvs_c": "c.959_969delTCATCAAGTGCinsGGACA",
"hgvs_p": "p.Ile320_Cys323delinsArgThr",
"transcript": "NM_001354346.2",
"protein_id": "NP_001341275.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 719,
"cds_start": 959,
"cds_end": null,
"cds_length": 2160,
"cdna_start": 1046,
"cdna_end": null,
"cdna_length": 2550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "IIKC",
"aa_alt": "RT",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"disruptive_inframe_deletion",
"splice_region_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"hgvs_c": "c.959_969delTCATCAAGTGCinsGGACA",
"hgvs_p": "p.Ile320_Cys323delinsArgThr",
"transcript": "ENST00000536053.6",
"protein_id": "ENSP00000444271.3",
"transcript_support_level": 2,
"aa_start": 320,
"aa_end": null,
"aa_length": 719,
"cds_start": 959,
"cds_end": null,
"cds_length": 2160,
"cdna_start": 1045,
"cdna_end": null,
"cdna_length": 2347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "IIKC",
"aa_alt": "RT",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"disruptive_inframe_deletion",
"splice_region_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"hgvs_c": "c.815_825delTCATCAAGTGCinsGGACA",
"hgvs_p": "p.Ile272_Cys275delinsArgThr",
"transcript": "ENST00000535233.6",
"protein_id": "ENSP00000438636.3",
"transcript_support_level": 2,
"aa_start": 272,
"aa_end": null,
"aa_length": 671,
"cds_start": 815,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 909,
"cdna_end": null,
"cdna_length": 2211,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "IIKC",
"aa_alt": "RT",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"disruptive_inframe_deletion",
"splice_region_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"hgvs_c": "c.11_21delTCATCAAGTGCinsGGACA",
"hgvs_p": "p.Ile4_Cys7delinsArgThr",
"transcript": "ENST00000649804.1",
"protein_id": "ENSP00000497938.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 351,
"cds_start": 11,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 21,
"cdna_end": null,
"cdna_length": 1107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"hgvs_c": "n.1982_1992delTCATCAAGTGCinsGGACA",
"hgvs_p": null,
"transcript": "ENST00000540394.5",
"protein_id": null,
"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": 3501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"hgvs_c": "n.889_899delTCATCAAGTGCinsGGACA",
"hgvs_p": null,
"transcript": "ENST00000648162.1",
"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": 1881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "C1R",
"gene_hgnc_id": 1246,
"dbsnp": "rs1057518646",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"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": 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": 6.416,
"phylop100way_prediction": "Uncertain_significance",
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM4,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PM4",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000647956.2",
"gene_symbol": "C1R",
"hgnc_id": 1246,
"effects": [
"missense_variant",
"disruptive_inframe_deletion",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.917_927delTCATCAAGTGCinsGGACA",
"hgvs_p": "p.Ile306_Cys309delinsArgThr"
}
],
"clinvar_disease": " periodontal type 1, periodontal type 2,Ehlers-Danlos syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Ehlers-Danlos syndrome, periodontal type 1|Ehlers-Danlos syndrome, periodontal type 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}