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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: 17-36537532-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=36537532&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 36537532,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000614443.2",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGW",
"gene_hgnc_id": 23213,
"hgvs_c": "c.431T>G",
"hgvs_p": "p.Ile144Ser",
"transcript": "NM_001346754.2",
"protein_id": "NP_001333683.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 504,
"cds_start": 431,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 1045,
"cdna_end": null,
"cdna_length": 2816,
"mane_select": "ENST00000614443.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGW",
"gene_hgnc_id": 23213,
"hgvs_c": "c.431T>G",
"hgvs_p": "p.Ile144Ser",
"transcript": "ENST00000614443.2",
"protein_id": "ENSP00000482202.1",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 504,
"cds_start": 431,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 1045,
"cdna_end": null,
"cdna_length": 2816,
"mane_select": "NM_001346754.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGW",
"gene_hgnc_id": 23213,
"hgvs_c": "c.431T>G",
"hgvs_p": "p.Ile144Ser",
"transcript": "ENST00000619326.1",
"protein_id": "ENSP00000480475.1",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 276,
"cds_start": 431,
"cds_end": null,
"cds_length": 833,
"cdna_start": 474,
"cdna_end": null,
"cdna_length": 876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGW",
"gene_hgnc_id": 23213,
"hgvs_c": "c.431T>G",
"hgvs_p": "p.Ile144Ser",
"transcript": "NM_001346755.2",
"protein_id": "NP_001333684.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 504,
"cds_start": 431,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 507,
"cdna_end": null,
"cdna_length": 2278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGW",
"gene_hgnc_id": 23213,
"hgvs_c": "c.431T>G",
"hgvs_p": "p.Ile144Ser",
"transcript": "NM_178517.5",
"protein_id": "NP_848612.2",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 504,
"cds_start": 431,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 2825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGW",
"gene_hgnc_id": 23213,
"hgvs_c": "c.431T>G",
"hgvs_p": "p.Ile144Ser",
"transcript": "ENST00000620233.1",
"protein_id": "ENSP00000480021.1",
"transcript_support_level": 2,
"aa_start": 144,
"aa_end": null,
"aa_length": 504,
"cds_start": 431,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 486,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MYO19",
"gene_hgnc_id": 26234,
"hgvs_c": "n.396-3428A>C",
"hgvs_p": null,
"transcript": "ENST00000610496.1",
"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": 578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MYO19",
"gene_hgnc_id": 26234,
"hgvs_c": "n.164-1899A>C",
"hgvs_p": null,
"transcript": "ENST00000617167.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MYO19",
"gene_hgnc_id": 26234,
"hgvs_c": "c.-295-3428A>C",
"hgvs_p": null,
"transcript": "XM_047436823.1",
"protein_id": "XP_047292779.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1047,
"cds_start": -4,
"cds_end": null,
"cds_length": 3144,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PIGW",
"gene_hgnc_id": 23213,
"dbsnp": "rs754061279",
"frequency_reference_population": 0.000005575911,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000478835,
"gnomad_genomes_af": 0.0000131403,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9013960361480713,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.776,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9044,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.48,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.432,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000614443.2",
"gene_symbol": "PIGW",
"hgnc_id": 23213,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.431T>G",
"hgvs_p": "p.Ile144Ser"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000610496.1",
"gene_symbol": "MYO19",
"hgnc_id": 26234,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.396-3428A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Hyperphosphatasia with intellectual disability syndrome 5,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Hyperphosphatasia with intellectual disability syndrome 5|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}