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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: 15-43048394-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=43048394&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP3",
"PP5"
],
"effects": [
"stop_gained",
"splice_region_variant"
],
"gene_symbol": "UBR1",
"hgnc_id": 16808,
"hgvs_c": "c.1537C>T",
"hgvs_p": "p.Gln513*",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_174916.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3,PP5",
"acmg_score": 12,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.66,
"chr": "15",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Johanson-Blizzard syndrome",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6600000262260437,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1749,
"aa_ref": "Q",
"aa_start": 513,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7698,
"cdna_start": 1553,
"cds_end": null,
"cds_length": 5250,
"cds_start": 1537,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 47,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_174916.3",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "c.1537C>T",
"hgvs_p": "p.Gln513*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000290650.9",
"protein_coding": true,
"protein_id": "NP_777576.1",
"strand": false,
"transcript": "NM_174916.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1749,
"aa_ref": "Q",
"aa_start": 513,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7698,
"cdna_start": 1553,
"cds_end": null,
"cds_length": 5250,
"cds_start": 1537,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 47,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000290650.9",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "c.1537C>T",
"hgvs_p": "p.Gln513*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_174916.3",
"protein_coding": true,
"protein_id": "ENSP00000290650.4",
"strand": false,
"transcript": "ENST00000290650.9",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1773,
"aa_ref": "Q",
"aa_start": 537,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5389,
"cdna_start": 1617,
"cds_end": null,
"cds_length": 5322,
"cds_start": 1609,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 48,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000914218.1",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "c.1609C>T",
"hgvs_p": "p.Gln537*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584277.1",
"strand": false,
"transcript": "ENST00000914218.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1741,
"aa_ref": "Q",
"aa_start": 513,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7666,
"cdna_start": 1545,
"cds_end": null,
"cds_length": 5226,
"cds_start": 1537,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 47,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000914217.1",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "c.1537C>T",
"hgvs_p": "p.Gln513*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584276.1",
"strand": false,
"transcript": "ENST00000914217.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1706,
"aa_ref": "Q",
"aa_start": 513,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7639,
"cdna_start": 1623,
"cds_end": null,
"cds_length": 5121,
"cds_start": 1537,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 46,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000914215.1",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "c.1537C>T",
"hgvs_p": "p.Gln513*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584274.1",
"strand": false,
"transcript": "ENST00000914215.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1672,
"aa_ref": "Q",
"aa_start": 513,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7462,
"cdna_start": 1548,
"cds_end": null,
"cds_length": 5019,
"cds_start": 1537,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 44,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000914216.1",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "c.1537C>T",
"hgvs_p": "p.Gln513*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584275.1",
"strand": false,
"transcript": "ENST00000914216.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1070,
"aa_ref": "Q",
"aa_start": 513,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3332,
"cdna_start": 1628,
"cds_end": null,
"cds_length": 3213,
"cds_start": 1537,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_count": 29,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000546274.6",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "c.1537C>T",
"hgvs_p": "p.Gln513*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000477932.1",
"strand": false,
"transcript": "ENST00000546274.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 721,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000569971.5",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "n.*189C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455759.1",
"strand": false,
"transcript": "ENST00000569971.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 721,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000569971.5",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "n.*189C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455759.1",
"strand": false,
"transcript": "ENST00000569971.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 545,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000563239.1",
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"hgvs_c": "n.*203-1105C>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000456502.1",
"strand": false,
"transcript": "ENST00000563239.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.998716718610971,
"dbsnp": "rs119477055",
"effect": "stop_gained,splice_region_variant",
"frequency_reference_population": 0.0000065763516,
"gene_hgnc_id": 16808,
"gene_symbol": "UBR1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657635,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Johanson-Blizzard syndrome",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.477,
"pos": 43048394,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9380000233650208,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.68,
"transcript": "NM_174916.3"
}
]
}