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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: 4-101032267-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=101032267&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Strong"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "PPP3CA",
"hgnc_id": 9314,
"hgvs_c": "c.1339G>T",
"hgvs_p": "p.Ala447Ser",
"inheritance_mode": "AD",
"pathogenic_score": 8,
"score": 8,
"transcript": "NM_000944.5",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong",
"acmg_score": 8,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.5234,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"chr": "4",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.32653307914733887,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 521,
"aa_ref": "A",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4743,
"cdna_start": 2069,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1339,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_000944.5",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.1339G>T",
"hgvs_p": "p.Ala447Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000394854.8",
"protein_coding": true,
"protein_id": "NP_000935.1",
"strand": false,
"transcript": "NM_000944.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 521,
"aa_ref": "A",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4743,
"cdna_start": 2069,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1339,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000394854.8",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.1339G>T",
"hgvs_p": "p.Ala447Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000944.5",
"protein_coding": true,
"protein_id": "ENSP00000378323.3",
"strand": false,
"transcript": "ENST00000394854.8",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 511,
"aa_ref": "A",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3604,
"cdna_start": 1870,
"cds_end": null,
"cds_length": 1536,
"cds_start": 1339,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000394853.8",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.1339G>T",
"hgvs_p": "p.Ala447Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000378322.4",
"strand": false,
"transcript": "ENST00000394853.8",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 469,
"aa_ref": "A",
"aa_start": 405,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4519,
"cdna_start": 1888,
"cds_end": null,
"cds_length": 1410,
"cds_start": 1213,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000323055.10",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.1213G>T",
"hgvs_p": "p.Ala405Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000320580.6",
"strand": false,
"transcript": "ENST00000323055.10",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 423,
"aa_ref": "A",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1958,
"cdna_start": 1184,
"cds_end": null,
"cds_length": 1272,
"cds_start": 1045,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000507176.5",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.1045G>T",
"hgvs_p": "p.Ala349Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000422990.1",
"strand": false,
"transcript": "ENST00000507176.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 289,
"aa_ref": "A",
"aa_start": 215,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4007,
"cdna_start": 1324,
"cds_end": null,
"cds_length": 870,
"cds_start": 643,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000512215.5",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.643G>T",
"hgvs_p": "p.Ala215Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000422781.1",
"strand": false,
"transcript": "ENST00000512215.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 511,
"aa_ref": "A",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4713,
"cdna_start": 2069,
"cds_end": null,
"cds_length": 1536,
"cds_start": 1339,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001130691.2",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.1339G>T",
"hgvs_p": "p.Ala447Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001124163.1",
"strand": false,
"transcript": "NM_001130691.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 479,
"aa_ref": "A",
"aa_start": 405,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4625,
"cdna_start": 1971,
"cds_end": null,
"cds_length": 1440,
"cds_start": 1213,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000964807.1",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.1213G>T",
"hgvs_p": "p.Ala405Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634866.1",
"strand": false,
"transcript": "ENST00000964807.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 469,
"aa_ref": "A",
"aa_start": 405,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4587,
"cdna_start": 1943,
"cds_end": null,
"cds_length": 1410,
"cds_start": 1213,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001130692.2",
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"hgvs_c": "c.1213G>T",
"hgvs_p": "p.Ala405Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001124164.1",
"strand": false,
"transcript": "NM_001130692.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999992397960259,
"dbsnp": "rs1553920374",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": 6.9293156e-7,
"gene_hgnc_id": 9314,
"gene_symbol": "PPP3CA",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.92932e-7,
"gnomad_exomes_homalt": 0,
"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": "Pathogenic",
"phylop100way_score": 7.624,
"pos": 101032267,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.259,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9940000176429749,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.6,
"transcript": "NM_000944.5"
}
]
}