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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-108681760-GT-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=108681760&ref=GT&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2"
],
"effects": [
"frameshift_variant",
"splice_region_variant"
],
"gene_symbol": "COL4A5",
"hgnc_id": 2207,
"hgvs_c": "c.4089delT",
"hgvs_p": "p.Pro1364fs",
"inheritance_mode": "XL",
"pathogenic_score": 10,
"score": 10,
"transcript": "NM_033380.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_score": 10,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "X",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1691,
"aa_ref": "G",
"aa_start": 1363,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6531,
"cdna_start": 4377,
"cds_end": null,
"cds_length": 5076,
"cds_start": 4089,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 53,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "NM_033380.3",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4089delT",
"hgvs_p": "p.Pro1364fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000328300.11",
"protein_coding": true,
"protein_id": "NP_203699.1",
"strand": true,
"transcript": "NM_033380.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1691,
"aa_ref": "G",
"aa_start": 1363,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6531,
"cdna_start": 4377,
"cds_end": null,
"cds_length": 5076,
"cds_start": 4089,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 53,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000328300.11",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4089delT",
"hgvs_p": "p.Pro1364fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_033380.3",
"protein_coding": true,
"protein_id": "ENSP00000331902.7",
"strand": true,
"transcript": "ENST00000328300.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1689,
"aa_ref": "G",
"aa_start": 1361,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6518,
"cdna_start": 4371,
"cds_end": null,
"cds_length": 5070,
"cds_start": 4083,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 51,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000949143.1",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4083delT",
"hgvs_p": "p.Pro1362fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619202.1",
"strand": true,
"transcript": "ENST00000949143.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1685,
"aa_ref": "G",
"aa_start": 1357,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6513,
"cdna_start": 4359,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4071,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 51,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "NM_000495.5",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4071delT",
"hgvs_p": "p.Pro1358fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_000486.1",
"strand": true,
"transcript": "NM_000495.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1685,
"aa_ref": "G",
"aa_start": 1357,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6427,
"cdna_start": 4273,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4071,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 51,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000361603.7",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4071delT",
"hgvs_p": "p.Pro1358fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000354505.2",
"strand": true,
"transcript": "ENST00000361603.7",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1685,
"aa_ref": "G",
"aa_start": 1357,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6398,
"cdna_start": 4242,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4071,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 52,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "ENST00000949141.1",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4071delT",
"hgvs_p": "p.Pro1358fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619200.1",
"strand": true,
"transcript": "ENST00000949141.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1671,
"aa_ref": "G",
"aa_start": 1343,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6492,
"cdna_start": 4340,
"cds_end": null,
"cds_length": 5016,
"cds_start": 4029,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 50,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "ENST00000949142.1",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4029delT",
"hgvs_p": "p.Pro1344fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619201.1",
"strand": true,
"transcript": "ENST00000949142.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1696,
"aa_ref": "G",
"aa_start": 1368,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6273,
"cdna_start": 4119,
"cds_end": null,
"cds_length": 5091,
"cds_start": 4104,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 54,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "XM_011530849.3",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4104delT",
"hgvs_p": "p.Pro1369fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011529151.2",
"strand": true,
"transcript": "XM_011530849.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1693,
"aa_ref": "G",
"aa_start": 1365,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6264,
"cdna_start": 4110,
"cds_end": null,
"cds_length": 5082,
"cds_start": 4095,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 53,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "XM_017029259.3",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4095delT",
"hgvs_p": "p.Pro1366fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884748.1",
"strand": true,
"transcript": "XM_017029259.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1690,
"aa_ref": "G",
"aa_start": 1362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6255,
"cdna_start": 4101,
"cds_end": null,
"cds_length": 5073,
"cds_start": 4086,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 52,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_017029260.2",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.4086delT",
"hgvs_p": "p.Pro1363fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884749.1",
"strand": true,
"transcript": "XM_017029260.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1583,
"aa_ref": "G",
"aa_start": 1255,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6583,
"cdna_start": 4429,
"cds_end": null,
"cds_length": 4752,
"cds_start": 3765,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 54,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "XM_047441810.1",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.3765delT",
"hgvs_p": "p.Pro1256fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047297766.1",
"strand": true,
"transcript": "XM_047441810.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 737,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000489230.1",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "n.492delT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000489230.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1581,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000510690.2",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "n.583delT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000510690.2",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 114,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 790,
"cdna_start": null,
"cds_end": null,
"cds_length": 345,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000515658.1",
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"hgvs_c": "c.-118delT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423520.1",
"strand": true,
"transcript": "ENST00000515658.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs104886268",
"effect": "frameshift_variant,splice_region_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 2207,
"gene_symbol": "COL4A5",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.042,
"pos": 108681760,
"ref": "GT",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_033380.3"
}
]
}