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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: 5-134158436-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=134158436&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 134158436,
"ref": "A",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000353411.11",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.475T>G",
"hgvs_p": "p.Cys159Gly",
"transcript": "ENST00000522552.5",
"protein_id": "ENSP00000429472.1",
"transcript_support_level": 1,
"aa_start": 159,
"aa_end": null,
"aa_length": 160,
"cds_start": 475,
"cds_end": null,
"cds_length": 483,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 1683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "n.1071T>G",
"hgvs_p": null,
"transcript": "ENST00000517691.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.456+19T>G",
"hgvs_p": null,
"transcript": "NM_170679.3",
"protein_id": "NP_733779.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9386,
"mane_select": "ENST00000353411.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.456+19T>G",
"hgvs_p": null,
"transcript": "ENST00000353411.11",
"protein_id": "ENSP00000231487.9",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9386,
"mane_select": "NM_170679.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272772",
"gene_hgnc_id": null,
"hgvs_c": "c.558+19T>G",
"hgvs_p": null,
"transcript": "ENST00000519718.2",
"protein_id": "ENSP00000430774.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 197,
"cds_start": -4,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.475T>G",
"hgvs_p": "p.Cys159Gly",
"transcript": "NM_006930.4",
"protein_id": "NP_008861.2",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 160,
"cds_start": 475,
"cds_end": null,
"cds_length": 483,
"cdna_start": 571,
"cdna_end": null,
"cdna_length": 2616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.456+19T>G",
"hgvs_p": null,
"transcript": "ENST00000517625.5",
"protein_id": "ENSP00000429961.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.456+19T>G",
"hgvs_p": null,
"transcript": "ENST00000521216.5",
"protein_id": "ENSP00000431067.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.456+19T>G",
"hgvs_p": null,
"transcript": "ENST00000522855.5",
"protein_id": "ENSP00000429686.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 802,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.456+19T>G",
"hgvs_p": null,
"transcript": "ENST00000328392.10",
"protein_id": "ENSP00000331708.6",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 157,
"cds_start": -4,
"cds_end": null,
"cds_length": 476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "n.*418+19T>G",
"hgvs_p": null,
"transcript": "ENST00000523966.5",
"protein_id": "ENSP00000429995.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "c.*48T>G",
"hgvs_p": null,
"transcript": "ENST00000519321.5",
"protein_id": "ENSP00000429415.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 141,
"cds_start": -4,
"cds_end": null,
"cds_length": 427,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"hgvs_c": "n.*421T>G",
"hgvs_p": null,
"transcript": "ENST00000519054.5",
"protein_id": "ENSP00000430885.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SKP1",
"gene_hgnc_id": 10899,
"dbsnp": "rs1114167278",
"frequency_reference_population": 0.0000013682736,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136827,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1251247227191925,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.013,
"revel_prediction": "Benign",
"alphamissense_score": 0.1368,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.039,
"phylop100way_prediction": "Benign",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000353411.11",
"gene_symbol": "SKP1",
"hgnc_id": 10899,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.456+19T>G",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000519718.2",
"gene_symbol": "ENSG00000272772",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.558+19T>G",
"hgvs_p": null
}
],
"clinvar_disease": "Keratoconus 1",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Keratoconus 1",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}