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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: 11-57389228-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=57389228&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRG2",
"hgnc_id": 9362,
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_002728.6",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ENSG00000254979",
"hgnc_id": null,
"hgvs_c": "c.463C>A",
"hgvs_p": "p.Pro155Thr",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -2,
"transcript": "ENST00000529411.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 385,
"alphamissense_prediction": null,
"alphamissense_score": 0.069,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.06999418139457703,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 222,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1431,
"cdna_start": 215,
"cds_end": null,
"cds_length": 669,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_002728.6",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000311862.10",
"protein_coding": true,
"protein_id": "NP_002719.3",
"strand": false,
"transcript": "NM_002728.6",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 222,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1431,
"cdna_start": 215,
"cds_end": null,
"cds_length": 669,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000311862.10",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002728.6",
"protein_coding": true,
"protein_id": "ENSP00000312134.5",
"strand": false,
"transcript": "ENST00000311862.10",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 226,
"aa_ref": "P",
"aa_start": 155,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 681,
"cdna_start": 463,
"cds_end": null,
"cds_length": 681,
"cds_start": 463,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000529411.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000254979",
"hgvs_c": "c.463C>A",
"hgvs_p": "p.Pro155Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000431536.1",
"strand": false,
"transcript": "ENST00000529411.1",
"transcript_support_level": 4
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 222,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1427,
"cdna_start": 211,
"cds_end": null,
"cds_length": 669,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001302926.2",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001289855.1",
"strand": false,
"transcript": "NM_001302926.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 222,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1544,
"cdna_start": 328,
"cds_end": null,
"cds_length": 669,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001302927.2",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001289856.1",
"strand": false,
"transcript": "NM_001302927.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 222,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1367,
"cdna_start": 314,
"cds_end": null,
"cds_length": 669,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000525955.1",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000433016.1",
"strand": false,
"transcript": "ENST00000525955.1",
"transcript_support_level": 2
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 222,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1111,
"cdna_start": 485,
"cds_end": null,
"cds_length": 669,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000886024.1",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556083.1",
"strand": false,
"transcript": "ENST00000886024.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 222,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 863,
"cdna_start": 235,
"cds_end": null,
"cds_length": 669,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000886025.1",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556084.1",
"strand": false,
"transcript": "ENST00000886025.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 211,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1398,
"cdna_start": 215,
"cds_end": null,
"cds_length": 636,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001243245.3",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001230174.1",
"strand": false,
"transcript": "NM_001243245.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 211,
"aa_ref": "P",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1350,
"cdna_start": 202,
"cds_end": null,
"cds_length": 636,
"cds_start": 148,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000533605.5",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "c.148C>A",
"hgvs_p": "p.Pro50Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000433231.1",
"strand": false,
"transcript": "ENST00000533605.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 533,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000528835.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000254979",
"hgvs_c": "n.*372C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000431480.1",
"strand": false,
"transcript": "ENST00000528835.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1048,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000530105.1",
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"hgvs_c": "n.194C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000530105.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1639,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000534081.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000254979",
"hgvs_c": "n.1008C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000534081.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 533,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000528835.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000254979",
"hgvs_c": "n.*372C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000431480.1",
"strand": false,
"transcript": "ENST00000528835.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs142628389",
"effect": "missense_variant",
"frequency_reference_population": 0.00023853956,
"gene_hgnc_id": 9362,
"gene_symbol": "PRG2",
"gnomad_exomes_ac": 357,
"gnomad_exomes_af": 0.000244207,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 28,
"gnomad_genomes_af": 0.000184072,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.362,
"pos": 57389228,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.029,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_002728.6"
}
]
}