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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: 15-38351477-CAG-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=38351477&ref=CAG&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "SPRED1",
"hgnc_id": 20249,
"hgvs_c": "c.1151_1152delAG",
"hgvs_p": "p.Glu384fs",
"inheritance_mode": "AD",
"pathogenic_score": 14,
"score": 14,
"transcript": "NM_152594.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Very_Strong",
"acmg_score": 14,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "15",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Legius syndrome,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 444,
"aa_ref": "E",
"aa_start": 384,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7270,
"cdna_start": 1501,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1151,
"consequences": [
"frameshift_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_152594.3",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1151_1152delAG",
"hgvs_p": "p.Glu384fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000299084.9",
"protein_coding": true,
"protein_id": "NP_689807.1",
"strand": true,
"transcript": "NM_152594.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 444,
"aa_ref": "E",
"aa_start": 384,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7270,
"cdna_start": 1501,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1151,
"consequences": [
"frameshift_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000299084.9",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1151_1152delAG",
"hgvs_p": "p.Glu384fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_152594.3",
"protein_coding": true,
"protein_id": "ENSP00000299084.4",
"strand": true,
"transcript": "ENST00000299084.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 456,
"aa_ref": "E",
"aa_start": 396,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5083,
"cdna_start": 1629,
"cds_end": null,
"cds_length": 1371,
"cds_start": 1187,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000881380.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1187_1188delAG",
"hgvs_p": "p.Glu396fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551439.1",
"strand": true,
"transcript": "ENST00000881380.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 451,
"aa_ref": "E",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4622,
"cdna_start": 2054,
"cds_end": null,
"cds_length": 1356,
"cds_start": 1172,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000951939.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1172_1173delAG",
"hgvs_p": "p.Glu391fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621998.1",
"strand": true,
"transcript": "ENST00000951939.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 444,
"aa_ref": "E",
"aa_start": 384,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3776,
"cdna_start": 1204,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1151,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000925370.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1151_1152delAG",
"hgvs_p": "p.Glu384fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595429.1",
"strand": true,
"transcript": "ENST00000925370.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 442,
"aa_ref": "E",
"aa_start": 382,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4608,
"cdna_start": 2056,
"cds_end": null,
"cds_length": 1329,
"cds_start": 1145,
"consequences": [
"frameshift_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000881381.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1145_1146delAG",
"hgvs_p": "p.Glu382fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551440.1",
"strand": true,
"transcript": "ENST00000881381.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 391,
"aa_ref": "E",
"aa_start": 331,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4546,
"cdna_start": 1977,
"cds_end": null,
"cds_length": 1176,
"cds_start": 992,
"consequences": [
"frameshift_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000951938.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.992_993delAG",
"hgvs_p": "p.Glu331fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621997.1",
"strand": true,
"transcript": "ENST00000951938.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 372,
"aa_ref": "E",
"aa_start": 312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4088,
"cdna_start": 1519,
"cds_end": null,
"cds_length": 1119,
"cds_start": 935,
"consequences": [
"frameshift_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000951940.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.935_936delAG",
"hgvs_p": "p.Glu312fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621999.1",
"strand": true,
"transcript": "ENST00000951940.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 319,
"aa_ref": "E",
"aa_start": 259,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4392,
"cdna_start": 1823,
"cds_end": null,
"cds_length": 960,
"cds_start": 776,
"consequences": [
"frameshift_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000951937.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.776_777delAG",
"hgvs_p": "p.Glu259fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621996.1",
"strand": true,
"transcript": "ENST00000951937.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 456,
"aa_ref": "E",
"aa_start": 396,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7306,
"cdna_start": 1537,
"cds_end": null,
"cds_length": 1371,
"cds_start": 1187,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_005254202.4",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1187_1188delAG",
"hgvs_p": "p.Glu396fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005254259.1",
"strand": true,
"transcript": "XM_005254202.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 423,
"aa_ref": "E",
"aa_start": 363,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7370,
"cdna_start": 1601,
"cds_end": null,
"cds_length": 1272,
"cds_start": 1088,
"consequences": [
"frameshift_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047432199.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1088_1089delAG",
"hgvs_p": "p.Glu363fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288155.1",
"strand": true,
"transcript": "XM_047432199.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 423,
"aa_ref": "E",
"aa_start": 363,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7334,
"cdna_start": 1565,
"cds_end": null,
"cds_length": 1272,
"cds_start": 1088,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047432200.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1088_1089delAG",
"hgvs_p": "p.Glu363fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288156.1",
"strand": true,
"transcript": "XM_047432200.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 423,
"aa_ref": "E",
"aa_start": 363,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7007,
"cdna_start": 1238,
"cds_end": null,
"cds_length": 1272,
"cds_start": 1088,
"consequences": [
"frameshift_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047432201.1",
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"hgvs_c": "c.1088_1089delAG",
"hgvs_p": "p.Glu363fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288157.1",
"strand": true,
"transcript": "XM_047432201.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs878855228",
"effect": "frameshift_variant",
"frequency_reference_population": 6.840591e-7,
"gene_hgnc_id": 20249,
"gene_symbol": "SPRED1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84059e-7,
"gnomad_exomes_homalt": 0,
"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": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Legius syndrome|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.993,
"pos": 38351477,
"ref": "CAG",
"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_152594.3"
}
]
}