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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: 2-189062913-AGCTCCCT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189062913&ref=AGCTCCCT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 189062913,
"ref": "AGCTCCCT",
"alt": "A",
"effect": "frameshift_variant,splice_acceptor_variant,splice_region_variant,intron_variant",
"transcript": "NM_000393.5",
"consequences": [
{
"aa_ref": "RGA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1924-2_1928delAGGGAGC",
"hgvs_p": "p.Gly642fs",
"transcript": "NM_000393.5",
"protein_id": "NP_000384.2",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 1499,
"cds_start": 1924,
"cds_end": null,
"cds_length": 4500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000374866.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000393.5"
},
{
"aa_ref": "RGA",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1924-2_1928delAGGGAGC",
"hgvs_p": "p.Gly642fs",
"transcript": "ENST00000374866.9",
"protein_id": "ENSP00000364000.3",
"transcript_support_level": 1,
"aa_start": 642,
"aa_end": null,
"aa_length": 1499,
"cds_start": 1924,
"cds_end": null,
"cds_length": 4500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000393.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374866.9"
},
{
"aa_ref": "RGA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1921-2_1925delAGGGAGC",
"hgvs_p": "p.Gly641fs",
"transcript": "ENST00000858728.1",
"protein_id": "ENSP00000528787.1",
"transcript_support_level": null,
"aa_start": 641,
"aa_end": null,
"aa_length": 1498,
"cds_start": 1921,
"cds_end": null,
"cds_length": 4497,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858728.1"
},
{
"aa_ref": "RGA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1924-2_1928delAGGGAGC",
"hgvs_p": "p.Gly642fs",
"transcript": "ENST00000858729.1",
"protein_id": "ENSP00000528788.1",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 1463,
"cds_start": 1924,
"cds_end": null,
"cds_length": 4392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858729.1"
},
{
"aa_ref": "RGA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.763-2_767delAGGGAGC",
"hgvs_p": "p.Gly255fs",
"transcript": "ENST00000618828.1",
"protein_id": "ENSP00000482184.1",
"transcript_support_level": 5,
"aa_start": 255,
"aa_end": null,
"aa_length": 1112,
"cds_start": 763,
"cds_end": null,
"cds_length": 3339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000618828.1"
},
{
"aa_ref": "RGA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1786-2_1790delAGGGAGC",
"hgvs_p": "p.Gly596fs",
"transcript": "XM_011510573.4",
"protein_id": "XP_011508875.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 1453,
"cds_start": 1786,
"cds_end": null,
"cds_length": 4362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510573.4"
},
{
"aa_ref": "RGA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1786-2_1790delAGGGAGC",
"hgvs_p": "p.Gly596fs",
"transcript": "XM_047443251.1",
"protein_id": "XP_047299207.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 1453,
"cds_start": 1786,
"cds_end": null,
"cds_length": 4362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443251.1"
},
{
"aa_ref": "RGA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "c.1786-2_1790delAGGGAGC",
"hgvs_p": "p.Gly596fs",
"transcript": "XM_047443252.1",
"protein_id": "XP_047299208.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 1453,
"cds_start": 1786,
"cds_end": null,
"cds_length": 4362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443252.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"hgvs_c": "n.30-2_34delAGGGAGC",
"hgvs_p": null,
"transcript": "ENST00000470524.2",
"protein_id": null,
"transcript_support_level": 5,
"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": "retained_intron",
"feature": "ENST00000470524.2"
}
],
"gene_symbol": "COL5A2",
"gene_hgnc_id": 2210,
"dbsnp": "rs786205103",
"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": 7.905,
"phylop100way_prediction": "Pathogenic",
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_000393.5",
"gene_symbol": "COL5A2",
"hgnc_id": 2210,
"effects": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1924-2_1928delAGGGAGC",
"hgvs_p": "p.Gly642fs"
}
],
"clinvar_disease": " classic type,Ehlers-Danlos syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Ehlers-Danlos syndrome, classic type",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}