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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: X-108687672-AAG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=108687672&ref=AAG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 108687672,
"ref": "AAG",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "NM_033380.3",
"consequences": [
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4509_4510delAG",
"hgvs_p": "p.Arg1503fs",
"transcript": "NM_033380.3",
"protein_id": "NP_203699.1",
"transcript_support_level": null,
"aa_start": 1503,
"aa_end": null,
"aa_length": 1691,
"cds_start": 4509,
"cds_end": null,
"cds_length": 5076,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000328300.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_033380.3"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4509_4510delAG",
"hgvs_p": "p.Arg1503fs",
"transcript": "ENST00000328300.11",
"protein_id": "ENSP00000331902.7",
"transcript_support_level": 1,
"aa_start": 1503,
"aa_end": null,
"aa_length": 1691,
"cds_start": 4509,
"cds_end": null,
"cds_length": 5076,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_033380.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000328300.11"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4503_4504delAG",
"hgvs_p": "p.Arg1501fs",
"transcript": "ENST00000949143.1",
"protein_id": "ENSP00000619202.1",
"transcript_support_level": null,
"aa_start": 1501,
"aa_end": null,
"aa_length": 1689,
"cds_start": 4503,
"cds_end": null,
"cds_length": 5070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949143.1"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4491_4492delAG",
"hgvs_p": "p.Arg1497fs",
"transcript": "NM_000495.5",
"protein_id": "NP_000486.1",
"transcript_support_level": null,
"aa_start": 1497,
"aa_end": null,
"aa_length": 1685,
"cds_start": 4491,
"cds_end": null,
"cds_length": 5058,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000495.5"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4491_4492delAG",
"hgvs_p": "p.Arg1497fs",
"transcript": "ENST00000361603.7",
"protein_id": "ENSP00000354505.2",
"transcript_support_level": 2,
"aa_start": 1497,
"aa_end": null,
"aa_length": 1685,
"cds_start": 4491,
"cds_end": null,
"cds_length": 5058,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361603.7"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4491_4492delAG",
"hgvs_p": "p.Arg1497fs",
"transcript": "ENST00000949141.1",
"protein_id": "ENSP00000619200.1",
"transcript_support_level": null,
"aa_start": 1497,
"aa_end": null,
"aa_length": 1685,
"cds_start": 4491,
"cds_end": null,
"cds_length": 5058,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949141.1"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4449_4450delAG",
"hgvs_p": "p.Arg1483fs",
"transcript": "ENST00000949142.1",
"protein_id": "ENSP00000619201.1",
"transcript_support_level": null,
"aa_start": 1483,
"aa_end": null,
"aa_length": 1671,
"cds_start": 4449,
"cds_end": null,
"cds_length": 5016,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949142.1"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.303_304delAG",
"hgvs_p": "p.Arg101fs",
"transcript": "ENST00000515658.1",
"protein_id": "ENSP00000423520.1",
"transcript_support_level": 5,
"aa_start": 101,
"aa_end": null,
"aa_length": 114,
"cds_start": 303,
"cds_end": null,
"cds_length": 345,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515658.1"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4524_4525delAG",
"hgvs_p": "p.Arg1508fs",
"transcript": "XM_011530849.3",
"protein_id": "XP_011529151.2",
"transcript_support_level": null,
"aa_start": 1508,
"aa_end": null,
"aa_length": 1696,
"cds_start": 4524,
"cds_end": null,
"cds_length": 5091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530849.3"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4515_4516delAG",
"hgvs_p": "p.Arg1505fs",
"transcript": "XM_017029259.3",
"protein_id": "XP_016884748.1",
"transcript_support_level": null,
"aa_start": 1505,
"aa_end": null,
"aa_length": 1693,
"cds_start": 4515,
"cds_end": null,
"cds_length": 5082,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029259.3"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4506_4507delAG",
"hgvs_p": "p.Arg1502fs",
"transcript": "XM_017029260.2",
"protein_id": "XP_016884749.1",
"transcript_support_level": null,
"aa_start": 1502,
"aa_end": null,
"aa_length": 1690,
"cds_start": 4506,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029260.2"
},
{
"aa_ref": "RA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.4185_4186delAG",
"hgvs_p": "p.Arg1395fs",
"transcript": "XM_047441810.1",
"protein_id": "XP_047297766.1",
"transcript_support_level": null,
"aa_start": 1395,
"aa_end": null,
"aa_length": 1583,
"cds_start": 4185,
"cds_end": null,
"cds_length": 4752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441810.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "n.1003_1004delAG",
"hgvs_p": null,
"transcript": "ENST00000510690.2",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000510690.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "n.*173_*174delAG",
"hgvs_p": null,
"transcript": "ENST00000489230.1",
"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": "ENST00000489230.1"
}
],
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"dbsnp": "rs104886421",
"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": 0.10999999940395355,
"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": 6.951,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.11,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "NM_033380.3",
"gene_symbol": "COL4A5",
"hgnc_id": 2207,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.4509_4510delAG",
"hgvs_p": "p.Arg1503fs"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}