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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: 13-66304742-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=66304742&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 66304742,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_203487.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3627C>T",
"hgvs_p": "p.Ser1209Ser",
"transcript": "NM_203487.3",
"protein_id": "NP_982354.1",
"transcript_support_level": null,
"aa_start": 1209,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3627,
"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": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3627C>T",
"hgvs_p": "p.Ser1209Ser",
"transcript": "ENST00000377865.7",
"protein_id": "ENSP00000367096.2",
"transcript_support_level": 1,
"aa_start": 1209,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3627,
"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": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3525C>T",
"hgvs_p": "p.Ser1175Ser",
"transcript": "ENST00000544246.5",
"protein_id": "ENSP00000442186.2",
"transcript_support_level": 1,
"aa_start": 1175,
"aa_end": null,
"aa_length": 1203,
"cds_start": 3525,
"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": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3501C>T",
"hgvs_p": "p.Ser1167Ser",
"transcript": "ENST00000456367.5",
"protein_id": "ENSP00000401699.2",
"transcript_support_level": 1,
"aa_start": 1167,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3501,
"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": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3525C>T",
"hgvs_p": "p.Ser1175Ser",
"transcript": "NM_020403.5",
"protein_id": "NP_065136.1",
"transcript_support_level": null,
"aa_start": 1175,
"aa_end": null,
"aa_length": 1203,
"cds_start": 3525,
"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": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3501C>T",
"hgvs_p": "p.Ser1167Ser",
"transcript": "NM_001318372.2",
"protein_id": "NP_001305301.1",
"transcript_support_level": null,
"aa_start": 1167,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3501,
"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": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3399C>T",
"hgvs_p": "p.Ser1133Ser",
"transcript": "NM_001318373.2",
"protein_id": "NP_001305302.1",
"transcript_support_level": null,
"aa_start": 1133,
"aa_end": null,
"aa_length": 1161,
"cds_start": 3399,
"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": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "c.3627C>T",
"hgvs_p": "p.Ser1209Ser",
"transcript": "XM_017020619.3",
"protein_id": "XP_016876108.1",
"transcript_support_level": null,
"aa_start": 1209,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3627,
"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": 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": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "n.421C>T",
"hgvs_p": null,
"transcript": "ENST00000617020.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000617020.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PCDH9-AS1",
"gene_hgnc_id": 39897,
"hgvs_c": "n.144+728G>A",
"hgvs_p": null,
"transcript": "ENST00000430861.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000430861.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PCDH9-AS1",
"gene_hgnc_id": 39897,
"hgvs_c": "n.144+728G>A",
"hgvs_p": null,
"transcript": "NR_046528.1",
"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": "NR_046528.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"hgvs_c": "n.*540C>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"
}
],
"gene_symbol": "PCDH9",
"gene_hgnc_id": 8661,
"dbsnp": "rs149158184",
"frequency_reference_population": 6.845189e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84519e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4699999988079071,
"computational_prediction_selected": "Benign",
"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": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.212,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_203487.3",
"gene_symbol": "PCDH9",
"hgnc_id": 8661,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3627C>T",
"hgvs_p": "p.Ser1209Ser"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000430861.1",
"gene_symbol": "PCDH9-AS1",
"hgnc_id": 39897,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.144+728G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}