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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: 13-66631254-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=66631254&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 66631254,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_203487.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3296C>T",
"hgvs_p": "p.Pro1099Leu",
"transcript": "NM_203487.3",
"protein_id": "NP_982354.1",
"transcript_support_level": null,
"aa_start": 1099,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3296,
"cds_end": null,
"cds_length": 3714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000377865.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_203487.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3296C>T",
"hgvs_p": "p.Pro1099Leu",
"transcript": "ENST00000377865.7",
"protein_id": "ENSP00000367096.2",
"transcript_support_level": 1,
"aa_start": 1099,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3296,
"cds_end": null,
"cds_length": 3714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_203487.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000377865.7"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3194C>T",
"hgvs_p": "p.Pro1065Leu",
"transcript": "ENST00000544246.5",
"protein_id": "ENSP00000442186.2",
"transcript_support_level": 1,
"aa_start": 1065,
"aa_end": null,
"aa_length": 1203,
"cds_start": 3194,
"cds_end": null,
"cds_length": 3612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544246.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3170C>T",
"hgvs_p": "p.Pro1057Leu",
"transcript": "ENST00000456367.5",
"protein_id": "ENSP00000401699.2",
"transcript_support_level": 1,
"aa_start": 1057,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3170,
"cds_end": null,
"cds_length": 3588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000456367.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "n.*209C>T",
"hgvs_p": null,
"transcript": "ENST00000614931.1",
"protein_id": "ENSP00000482917.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000614931.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "n.*209C>T",
"hgvs_p": null,
"transcript": "ENST00000614931.1",
"protein_id": "ENSP00000482917.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000614931.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3194C>T",
"hgvs_p": "p.Pro1065Leu",
"transcript": "NM_020403.5",
"protein_id": "NP_065136.1",
"transcript_support_level": null,
"aa_start": 1065,
"aa_end": null,
"aa_length": 1203,
"cds_start": 3194,
"cds_end": null,
"cds_length": 3612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020403.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3170C>T",
"hgvs_p": "p.Pro1057Leu",
"transcript": "NM_001318372.2",
"protein_id": "NP_001305301.1",
"transcript_support_level": null,
"aa_start": 1057,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3170,
"cds_end": null,
"cds_length": 3588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318372.2"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3068C>T",
"hgvs_p": "p.Pro1023Leu",
"transcript": "NM_001318373.2",
"protein_id": "NP_001305302.1",
"transcript_support_level": null,
"aa_start": 1023,
"aa_end": null,
"aa_length": 1161,
"cds_start": 3068,
"cds_end": null,
"cds_length": 3486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318373.2"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3296C>T",
"hgvs_p": "p.Pro1099Leu",
"transcript": "XM_017020619.3",
"protein_id": "XP_016876108.1",
"transcript_support_level": null,
"aa_start": 1099,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3296,
"cds_end": null,
"cds_length": 3714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017020619.3"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "LOC105370247",
"gene_hgnc_id": null,
"hgvs_c": "n.169-28807G>A",
"hgvs_p": null,
"transcript": "XR_007063818.1",
"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_007063818.1"
}
],
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"dbsnp": "rs145894829",
"frequency_reference_population": 0.000787518,
"hom_count_reference_population": 4,
"allele_count_reference_population": 1268,
"gnomad_exomes_af": 0.000794313,
"gnomad_genomes_af": 0.000722458,
"gnomad_exomes_ac": 1158,
"gnomad_genomes_ac": 110,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01951456069946289,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.313,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5351,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.17,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.556,
"phylop100way_prediction": "Pathogenic",
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_203487.3",
"gene_symbol": "PCDH9",
"hgnc_id": 8661,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3296C>T",
"hgvs_p": "p.Pro1099Leu"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_007063818.1",
"gene_symbol": "LOC105370247",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.169-28807G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}