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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: 11-72584902-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=72584902&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 72584902,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_002599.5",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1329G>A",
"hgvs_p": "p.Lys443Lys",
"transcript": "NM_002599.5",
"protein_id": "NP_002590.1",
"transcript_support_level": null,
"aa_start": 443,
"aa_end": null,
"aa_length": 941,
"cds_start": 1329,
"cds_end": null,
"cds_length": 2826,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000334456.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002599.5"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1329G>A",
"hgvs_p": "p.Lys443Lys",
"transcript": "ENST00000334456.10",
"protein_id": "ENSP00000334910.5",
"transcript_support_level": 1,
"aa_start": 443,
"aa_end": null,
"aa_length": 941,
"cds_start": 1329,
"cds_end": null,
"cds_length": 2826,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002599.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334456.10"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1302G>A",
"hgvs_p": "p.Lys434Lys",
"transcript": "ENST00000540345.5",
"protein_id": "ENSP00000446399.1",
"transcript_support_level": 1,
"aa_start": 434,
"aa_end": null,
"aa_length": 932,
"cds_start": 1302,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540345.5"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1308G>A",
"hgvs_p": "p.Lys436Lys",
"transcript": "NM_001143839.4",
"protein_id": "NP_001137311.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 934,
"cds_start": 1308,
"cds_end": null,
"cds_length": 2805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001143839.4"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1308G>A",
"hgvs_p": "p.Lys436Lys",
"transcript": "ENST00000544570.5",
"protein_id": "ENSP00000442256.1",
"transcript_support_level": 5,
"aa_start": 436,
"aa_end": null,
"aa_length": 934,
"cds_start": 1308,
"cds_end": null,
"cds_length": 2805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544570.5"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1302G>A",
"hgvs_p": "p.Lys434Lys",
"transcript": "NM_001146209.3",
"protein_id": "NP_001139681.1",
"transcript_support_level": null,
"aa_start": 434,
"aa_end": null,
"aa_length": 932,
"cds_start": 1302,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001146209.3"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1266G>A",
"hgvs_p": "p.Lys422Lys",
"transcript": "NM_001243784.2",
"protein_id": "NP_001230713.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 920,
"cds_start": 1266,
"cds_end": null,
"cds_length": 2763,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001243784.2"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1266G>A",
"hgvs_p": "p.Lys422Lys",
"transcript": "ENST00000444035.6",
"protein_id": "ENSP00000411657.3",
"transcript_support_level": 5,
"aa_start": 422,
"aa_end": null,
"aa_length": 920,
"cds_start": 1266,
"cds_end": null,
"cds_length": 2763,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000444035.6"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.984G>A",
"hgvs_p": "p.Lys328Lys",
"transcript": "ENST00000418754.6",
"protein_id": "ENSP00000410310.2",
"transcript_support_level": 2,
"aa_start": 328,
"aa_end": null,
"aa_length": 826,
"cds_start": 984,
"cds_end": null,
"cds_length": 2481,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000418754.6"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.561G>A",
"hgvs_p": "p.Lys187Lys",
"transcript": "ENST00000376450.7",
"protein_id": "ENSP00000365633.3",
"transcript_support_level": 2,
"aa_start": 187,
"aa_end": null,
"aa_length": 685,
"cds_start": 561,
"cds_end": null,
"cds_length": 2058,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376450.7"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.801G>A",
"hgvs_p": "p.Lys267Lys",
"transcript": "ENST00000475807.6",
"protein_id": "ENSP00000439077.1",
"transcript_support_level": 3,
"aa_start": 267,
"aa_end": null,
"aa_length": 335,
"cds_start": 801,
"cds_end": null,
"cds_length": 1009,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000475807.6"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "c.1326G>A",
"hgvs_p": "p.Lys442Lys",
"transcript": "XM_005274040.4",
"protein_id": "XP_005274097.1",
"transcript_support_level": null,
"aa_start": 442,
"aa_end": null,
"aa_length": 940,
"cds_start": 1326,
"cds_end": null,
"cds_length": 2823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005274040.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "n.*1172G>A",
"hgvs_p": null,
"transcript": "ENST00000539367.5",
"protein_id": "ENSP00000445443.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000539367.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A-AS2",
"gene_hgnc_id": 40434,
"hgvs_c": "n.394C>T",
"hgvs_p": null,
"transcript": "ENST00000545254.2",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000545254.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A-AS2",
"gene_hgnc_id": 40434,
"hgvs_c": "n.297C>T",
"hgvs_p": null,
"transcript": "XR_001748291.2",
"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_001748291.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"hgvs_c": "n.*1172G>A",
"hgvs_p": null,
"transcript": "ENST00000539367.5",
"protein_id": "ENSP00000445443.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000539367.5"
}
],
"gene_symbol": "PDE2A",
"gene_hgnc_id": 8777,
"dbsnp": "rs199979190",
"frequency_reference_population": 0.00004088733,
"hom_count_reference_population": 0,
"allele_count_reference_population": 66,
"gnomad_exomes_af": 0.000040359,
"gnomad_genomes_af": 0.0000459583,
"gnomad_exomes_ac": 59,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.30000001192092896,
"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": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.145,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_002599.5",
"gene_symbol": "PDE2A",
"hgnc_id": 8777,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1329G>A",
"hgvs_p": "p.Lys443Lys"
},
{
"score": -8,
"benign_score": 10,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000545254.2",
"gene_symbol": "PDE2A-AS2",
"hgnc_id": 40434,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.394C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}