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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: 17-40863123-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=40863123&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 40863123,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000223.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT12",
"gene_hgnc_id": 6414,
"hgvs_c": "c.1316G>A",
"hgvs_p": "p.Gly439Asp",
"transcript": "NM_000223.4",
"protein_id": "NP_000214.1",
"transcript_support_level": null,
"aa_start": 439,
"aa_end": null,
"aa_length": 494,
"cds_start": 1316,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 1353,
"cdna_end": null,
"cdna_length": 1880,
"mane_select": "ENST00000251643.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT12",
"gene_hgnc_id": 6414,
"hgvs_c": "c.1316G>A",
"hgvs_p": "p.Gly439Asp",
"transcript": "ENST00000251643.5",
"protein_id": "ENSP00000251643.4",
"transcript_support_level": 1,
"aa_start": 439,
"aa_end": null,
"aa_length": 494,
"cds_start": 1316,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 1353,
"cdna_end": null,
"cdna_length": 1880,
"mane_select": "NM_000223.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "ENSG00000265359",
"gene_hgnc_id": null,
"hgvs_c": "n.99C>T",
"hgvs_p": null,
"transcript": "ENST00000579136.1",
"protein_id": null,
"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": 258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT12",
"gene_hgnc_id": 6414,
"hgvs_c": "n.608G>A",
"hgvs_p": null,
"transcript": "ENST00000648535.1",
"protein_id": null,
"transcript_support_level": null,
"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": 614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "ENSG00000265359",
"gene_hgnc_id": null,
"hgvs_c": "n.61+12263C>T",
"hgvs_p": null,
"transcript": "ENST00000818906.1",
"protein_id": null,
"transcript_support_level": null,
"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": 651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "LOC105371777",
"gene_hgnc_id": null,
"hgvs_c": "n.63+12263C>T",
"hgvs_p": null,
"transcript": "XR_934754.3",
"protein_id": null,
"transcript_support_level": null,
"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": 284,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KRT12",
"gene_hgnc_id": 6414,
"hgvs_c": "n.*199G>A",
"hgvs_p": null,
"transcript": "ENST00000650597.1",
"protein_id": null,
"transcript_support_level": null,
"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": 588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KRT12",
"gene_hgnc_id": 6414,
"dbsnp": "rs1305982561",
"frequency_reference_population": 0.000023545303,
"hom_count_reference_population": 0,
"allele_count_reference_population": 38,
"gnomad_exomes_af": 0.0000253136,
"gnomad_genomes_af": 0.00000656832,
"gnomad_exomes_ac": 37,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5150758624076843,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9879999756813049,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.412,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.092,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.775,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.16,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999919195303656,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_000223.4",
"gene_symbol": "KRT12",
"hgnc_id": 6414,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1316G>A",
"hgvs_p": "p.Gly439Asp"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000579136.1",
"gene_symbol": "ENSG00000265359",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.99C>T",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_934754.3",
"gene_symbol": "LOC105371777",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.63+12263C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}