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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: 4-88277203-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=88277203&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 88277203,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000608933.6",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "NM_152542.5",
"protein_id": "NP_689755.3",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 372,
"cds_start": 481,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 6309,
"mane_select": "ENST00000608933.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "ENST00000608933.6",
"protein_id": "ENSP00000477341.1",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 372,
"cds_start": 481,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 6309,
"mane_select": "NM_152542.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "ENST00000514204.1",
"protein_id": "ENSP00000477241.1",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 182,
"cds_start": 481,
"cds_end": null,
"cds_length": 549,
"cdna_start": 904,
"cdna_end": null,
"cdna_length": 2962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "n.696A>G",
"hgvs_p": null,
"transcript": "ENST00000506423.1",
"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": 1091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "ENST00000295908.11",
"protein_id": "ENSP00000295908.7",
"transcript_support_level": 5,
"aa_start": 161,
"aa_end": null,
"aa_length": 327,
"cds_start": 481,
"cds_end": null,
"cds_length": 984,
"cdna_start": 713,
"cdna_end": null,
"cdna_length": 1940,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "XM_006714111.5",
"protein_id": "XP_006714174.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 372,
"cds_start": 481,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 991,
"cdna_end": null,
"cdna_length": 6604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "XM_017007803.3",
"protein_id": "XP_016863292.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 372,
"cds_start": 481,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 6199,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "XM_005262775.5",
"protein_id": "XP_005262832.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 193,
"cds_start": 481,
"cds_end": null,
"cds_length": 582,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 2607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "XM_047449673.1",
"protein_id": "XP_047305629.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 193,
"cds_start": 481,
"cds_end": null,
"cds_length": 582,
"cdna_start": 991,
"cdna_end": null,
"cdna_length": 2902,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "XM_047449674.1",
"protein_id": "XP_047305630.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 193,
"cds_start": 481,
"cds_end": null,
"cds_length": 582,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala",
"transcript": "XM_047449675.1",
"protein_id": "XP_047305631.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 193,
"cds_start": 481,
"cds_end": null,
"cds_length": 582,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "n.365A>G",
"hgvs_p": null,
"transcript": "ENST00000511506.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "n.2498A>G",
"hgvs_p": null,
"transcript": "ENST00000513546.3",
"protein_id": null,
"transcript_support_level": 6,
"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": 4777,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.-177A>G",
"hgvs_p": null,
"transcript": "ENST00000508256.5",
"protein_id": "ENSP00000476452.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": -4,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 923,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.-177A>G",
"hgvs_p": null,
"transcript": "ENST00000510548.6",
"protein_id": "ENSP00000476789.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 20,
"cds_start": -4,
"cds_end": null,
"cds_length": 63,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.-40A>G",
"hgvs_p": null,
"transcript": "XM_017007806.3",
"protein_id": "XP_016863295.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 263,
"cds_start": -4,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"hgvs_c": "c.-40A>G",
"hgvs_p": null,
"transcript": "XM_047449672.1",
"protein_id": "XP_047305628.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 263,
"cds_start": -4,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PPM1K",
"gene_hgnc_id": 25415,
"dbsnp": "rs113436519",
"frequency_reference_population": 0.0005656957,
"hom_count_reference_population": 2,
"allele_count_reference_population": 913,
"gnomad_exomes_af": 0.000311261,
"gnomad_genomes_af": 0.00301027,
"gnomad_exomes_ac": 455,
"gnomad_genomes_ac": 458,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005887627601623535,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.054,
"revel_prediction": "Benign",
"alphamissense_score": 0.0762,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.05,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000608933.6",
"gene_symbol": "PPM1K",
"hgnc_id": 25415,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.481A>G",
"hgvs_p": "p.Thr161Ala"
}
],
"clinvar_disease": " mild variant,Maple syrup urine disease",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Maple syrup urine disease, mild variant",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}