← Back to variant description
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: 2-188991716-GGCTGCAGTGAGTATA-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=188991716&ref=GGCTGCAGTGAGTATA&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 188991716,
"ref": "GGCTGCAGTGAGTATA",
"alt": "G",
"effect": "splice_donor_variant,conservative_inframe_deletion,splice_region_variant,intron_variant",
"transcript": "ENST00000304636.9",
"consequences": [
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.951_951+14delAGTGAGTATAGCTGC",
"hgvs_p": "p.Gly318fs",
"transcript": "NM_000090.4",
"protein_id": "NP_000081.2",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 1466,
"cds_start": 951,
"cds_end": null,
"cds_length": 4401,
"cdna_start": 1068,
"cdna_end": null,
"cdna_length": 5490,
"mane_select": "ENST00000304636.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AA",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.946_951+9delGCTGCAGTGAGTATA",
"hgvs_p": "p.Ala316_Ala317del",
"transcript": "ENST00000304636.9",
"protein_id": "ENSP00000304408.4",
"transcript_support_level": 1,
"aa_start": 316,
"aa_end": null,
"aa_length": 1466,
"cds_start": 946,
"cds_end": null,
"cds_length": 4401,
"cdna_start": 1063,
"cdna_end": null,
"cdna_length": 5490,
"mane_select": "NM_000090.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.946_951+9delGCTGCAGTGAGTATA",
"hgvs_p": "p.Ala316_Ala317del",
"transcript": "ENST00000450867.2",
"protein_id": "ENSP00000415346.2",
"transcript_support_level": 1,
"aa_start": 316,
"aa_end": null,
"aa_length": 1433,
"cds_start": 946,
"cds_end": null,
"cds_length": 4302,
"cdna_start": 1063,
"cdna_end": null,
"cdna_length": 5391,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.946_951+9delGCTGCAGTGAGTATA",
"hgvs_p": "p.Ala316_Ala317del",
"transcript": "ENST00000713745.1",
"protein_id": "ENSP00000519049.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 1415,
"cds_start": 946,
"cds_end": null,
"cds_length": 4248,
"cdna_start": 1063,
"cdna_end": null,
"cdna_length": 5337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.946_951+9delGCTGCAGTGAGTATA",
"hgvs_p": "p.Ala316_Ala317del",
"transcript": "ENST00000713744.1",
"protein_id": "ENSP00000519048.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 1412,
"cds_start": 946,
"cds_end": null,
"cds_length": 4239,
"cdna_start": 1063,
"cdna_end": null,
"cdna_length": 5328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"dbsnp": "rs587779425",
"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": 7.264,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PVS1_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000304636.9",
"gene_symbol": "COL3A1",
"hgnc_id": 2201,
"effects": [
"splice_donor_variant",
"conservative_inframe_deletion",
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.946_951+9delGCTGCAGTGAGTATA",
"hgvs_p": "p.Ala316_Ala317del"
}
],
"clinvar_disease": " type 4,Ehlers-Danlos syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Ehlers-Danlos syndrome, type 4",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}