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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: 2-227991070-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227991070&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227991070,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_001142644.2",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "c.4889G>A",
"hgvs_p": "p.Trp1630*",
"transcript": "NM_001142644.2",
"protein_id": "NP_001136116.1",
"transcript_support_level": null,
"aa_start": 1630,
"aa_end": null,
"aa_length": 1700,
"cds_start": 4889,
"cds_end": null,
"cds_length": 5103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000392056.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142644.2"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "c.4889G>A",
"hgvs_p": "p.Trp1630*",
"transcript": "ENST00000392056.8",
"protein_id": "ENSP00000375909.3",
"transcript_support_level": 1,
"aa_start": 1630,
"aa_end": null,
"aa_length": 1700,
"cds_start": 4889,
"cds_end": null,
"cds_length": 5103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001142644.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392056.8"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "c.4802G>A",
"hgvs_p": "p.Trp1601*",
"transcript": "ENST00000344657.5",
"protein_id": "ENSP00000339886.5",
"transcript_support_level": 1,
"aa_start": 1601,
"aa_end": null,
"aa_length": 1671,
"cds_start": 4802,
"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": "ENST00000344657.5"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "c.4802G>A",
"hgvs_p": "p.Trp1601*",
"transcript": "NM_030623.4",
"protein_id": "NP_085126.2",
"transcript_support_level": null,
"aa_start": 1601,
"aa_end": null,
"aa_length": 1671,
"cds_start": 4802,
"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": "NM_030623.4"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "c.4964G>A",
"hgvs_p": "p.Trp1655*",
"transcript": "XM_006712777.4",
"protein_id": "XP_006712840.1",
"transcript_support_level": null,
"aa_start": 1655,
"aa_end": null,
"aa_length": 1725,
"cds_start": 4964,
"cds_end": null,
"cds_length": 5178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712777.4"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "c.4934G>A",
"hgvs_p": "p.Trp1645*",
"transcript": "XM_011511925.3",
"protein_id": "XP_011510227.1",
"transcript_support_level": null,
"aa_start": 1645,
"aa_end": null,
"aa_length": 1715,
"cds_start": 4934,
"cds_end": null,
"cds_length": 5148,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511925.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "c.4877G>A",
"hgvs_p": "p.Trp1626*",
"transcript": "XM_006712778.5",
"protein_id": "XP_006712841.1",
"transcript_support_level": null,
"aa_start": 1626,
"aa_end": null,
"aa_length": 1696,
"cds_start": 4877,
"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_006712778.5"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "c.4838G>A",
"hgvs_p": "p.Trp1613*",
"transcript": "XM_005246870.5",
"protein_id": "XP_005246927.1",
"transcript_support_level": null,
"aa_start": 1613,
"aa_end": null,
"aa_length": 1683,
"cds_start": 4838,
"cds_end": null,
"cds_length": 5052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005246870.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"hgvs_c": "n.382G>A",
"hgvs_p": null,
"transcript": "ENST00000490603.1",
"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": "ENST00000490603.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105373918",
"gene_hgnc_id": null,
"hgvs_c": "n.146+28323C>T",
"hgvs_p": null,
"transcript": "XR_001739908.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "XR_001739908.2"
}
],
"gene_symbol": "SPHKAP",
"gene_hgnc_id": 30619,
"dbsnp": null,
"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": 0.6600000262260437,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.66,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.277,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001142644.2",
"gene_symbol": "SPHKAP",
"hgnc_id": 30619,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4889G>A",
"hgvs_p": "p.Trp1630*"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_001739908.2",
"gene_symbol": "LOC105373918",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.146+28323C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}