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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: 16-28902590-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28902590&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "ATP2A1",
"hgnc_id": 811,
"hgvs_c": "c.2535T>A",
"hgvs_p": "p.Gly845Gly",
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_173201.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_score": -3,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.5,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 994,
"aa_ref": "G",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3493,
"cdna_start": 2719,
"cds_end": null,
"cds_length": 2985,
"cds_start": 2535,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_004320.6",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2535T>A",
"hgvs_p": "p.Gly845Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000395503.9",
"protein_coding": true,
"protein_id": "NP_004311.1",
"strand": true,
"transcript": "NM_004320.6",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 994,
"aa_ref": "G",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3493,
"cdna_start": 2719,
"cds_end": null,
"cds_length": 2985,
"cds_start": 2535,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000395503.9",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2535T>A",
"hgvs_p": "p.Gly845Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004320.6",
"protein_coding": true,
"protein_id": "ENSP00000378879.5",
"strand": true,
"transcript": "ENST00000395503.9",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1005,
"aa_ref": "G",
"aa_start": 856,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3522,
"cdna_start": 2752,
"cds_end": null,
"cds_length": 3018,
"cds_start": 2568,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000971328.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2568T>A",
"hgvs_p": "p.Gly856Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641387.1",
"strand": true,
"transcript": "ENST00000971328.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1001,
"aa_ref": "G",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3451,
"cdna_start": 2719,
"cds_end": null,
"cds_length": 3006,
"cds_start": 2535,
"consequences": [
"synonymous_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_173201.5",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2535T>A",
"hgvs_p": "p.Gly845Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_775293.1",
"strand": true,
"transcript": "NM_173201.5",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1001,
"aa_ref": "G",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3532,
"cdna_start": 2802,
"cds_end": null,
"cds_length": 3006,
"cds_start": 2535,
"consequences": [
"synonymous_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000357084.7",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2535T>A",
"hgvs_p": "p.Gly845Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000349595.3",
"strand": true,
"transcript": "ENST00000357084.7",
"transcript_support_level": 2
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 994,
"aa_ref": "G",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3487,
"cdna_start": 2719,
"cds_end": null,
"cds_length": 2985,
"cds_start": 2535,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000971325.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2535T>A",
"hgvs_p": "p.Gly845Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641384.1",
"strand": true,
"transcript": "ENST00000971325.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 988,
"aa_ref": "G",
"aa_start": 839,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3468,
"cdna_start": 2696,
"cds_end": null,
"cds_length": 2967,
"cds_start": 2517,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000971329.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2517T>A",
"hgvs_p": "p.Gly839Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641388.1",
"strand": true,
"transcript": "ENST00000971329.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 967,
"aa_ref": "G",
"aa_start": 818,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3411,
"cdna_start": 2638,
"cds_end": null,
"cds_length": 2904,
"cds_start": 2454,
"consequences": [
"synonymous_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000971326.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2454T>A",
"hgvs_p": "p.Gly818Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641385.1",
"strand": true,
"transcript": "ENST00000971326.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 961,
"aa_ref": "G",
"aa_start": 812,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3391,
"cdna_start": 2619,
"cds_end": null,
"cds_length": 2886,
"cds_start": 2436,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000971327.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2436T>A",
"hgvs_p": "p.Gly812Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641386.1",
"strand": true,
"transcript": "ENST00000971327.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 869,
"aa_ref": "G",
"aa_start": 720,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3142,
"cdna_start": 2368,
"cds_end": null,
"cds_length": 2610,
"cds_start": 2160,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_001286075.2",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2160T>A",
"hgvs_p": "p.Gly720Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001273004.1",
"strand": true,
"transcript": "NM_001286075.2",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 869,
"aa_ref": "G",
"aa_start": 720,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 2358,
"cds_end": null,
"cds_length": 2610,
"cds_start": 2160,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000536376.5",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2160T>A",
"hgvs_p": "p.Gly720Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443101.1",
"strand": true,
"transcript": "ENST00000536376.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1291666603",
"effect": "synonymous_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.437,
"pos": 28902590,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_173201.5"
}
]
}