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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: 12-57726635-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57726635&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57726635,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001122772.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.3496A>G",
"hgvs_p": "p.Ser1166Gly",
"transcript": "NM_001122772.3",
"protein_id": "NP_001116244.1",
"transcript_support_level": null,
"aa_start": 1166,
"aa_end": null,
"aa_length": 1192,
"cds_start": 3496,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 3992,
"cdna_end": null,
"cdna_length": 5430,
"mane_select": "ENST00000547588.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.3496A>G",
"hgvs_p": "p.Ser1166Gly",
"transcript": "ENST00000547588.6",
"protein_id": "ENSP00000449241.1",
"transcript_support_level": 1,
"aa_start": 1166,
"aa_end": null,
"aa_length": 1192,
"cds_start": 3496,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 3992,
"cdna_end": null,
"cdna_length": 5430,
"mane_select": "NM_001122772.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.2428A>G",
"hgvs_p": "p.Ser810Gly",
"transcript": "ENST00000257897.7",
"protein_id": "ENSP00000257897.3",
"transcript_support_level": 1,
"aa_start": 810,
"aa_end": null,
"aa_length": 836,
"cds_start": 2428,
"cds_end": null,
"cds_length": 2511,
"cdna_start": 2514,
"cdna_end": null,
"cdna_length": 5388,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AGAP2-AS1",
"gene_hgnc_id": 48633,
"hgvs_c": "n.108+257T>C",
"hgvs_p": null,
"transcript": "ENST00000542466.2",
"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": 1500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.3025A>G",
"hgvs_p": "p.Ser1009Gly",
"transcript": "ENST00000328568.9",
"protein_id": "ENSP00000328160.4",
"transcript_support_level": 5,
"aa_start": 1009,
"aa_end": null,
"aa_length": 1035,
"cds_start": 3025,
"cds_end": null,
"cds_length": 3108,
"cdna_start": 3026,
"cdna_end": null,
"cdna_length": 4464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.2428A>G",
"hgvs_p": "p.Ser810Gly",
"transcript": "NM_014770.4",
"protein_id": "NP_055585.1",
"transcript_support_level": null,
"aa_start": 810,
"aa_end": null,
"aa_length": 836,
"cds_start": 2428,
"cds_end": null,
"cds_length": 2511,
"cdna_start": 2518,
"cdna_end": null,
"cdna_length": 5392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.3436A>G",
"hgvs_p": "p.Ser1146Gly",
"transcript": "XM_005268625.4",
"protein_id": "XP_005268682.1",
"transcript_support_level": null,
"aa_start": 1146,
"aa_end": null,
"aa_length": 1172,
"cds_start": 3436,
"cds_end": null,
"cds_length": 3519,
"cdna_start": 3932,
"cdna_end": null,
"cdna_length": 6806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.2488A>G",
"hgvs_p": "p.Ser830Gly",
"transcript": "XM_005268626.3",
"protein_id": "XP_005268683.1",
"transcript_support_level": null,
"aa_start": 830,
"aa_end": null,
"aa_length": 856,
"cds_start": 2488,
"cds_end": null,
"cds_length": 2571,
"cdna_start": 2578,
"cdna_end": null,
"cdna_length": 5452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "OS9",
"gene_hgnc_id": 16994,
"hgvs_c": "c.287-330T>C",
"hgvs_p": null,
"transcript": "ENST00000700670.1",
"protein_id": "ENSP00000515138.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 104,
"cds_start": -4,
"cds_end": null,
"cds_length": 315,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1666,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AGAP2-AS1",
"gene_hgnc_id": 48633,
"hgvs_c": "n.139+257T>C",
"hgvs_p": null,
"transcript": "NR_027032.1",
"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": 1531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"dbsnp": "rs936895004",
"frequency_reference_population": 0.0000047744547,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000477445,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07788589596748352,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.035,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.172,
"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": "NM_001122772.3",
"gene_symbol": "AGAP2",
"hgnc_id": 16921,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3496A>G",
"hgvs_p": "p.Ser1166Gly"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000542466.2",
"gene_symbol": "AGAP2-AS1",
"hgnc_id": 48633,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.108+257T>C",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000700670.1",
"gene_symbol": "OS9",
"hgnc_id": 16994,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.287-330T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}