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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: 17-36537312-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=36537312&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"PP5",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PIGW",
"hgnc_id": 23213,
"hgvs_c": "c.211A>C",
"hgvs_p": "p.Thr71Pro",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 2,
"transcript": "NM_178517.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 1,
"criteria": [
"PM2",
"PP5",
"BP4"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MYO19",
"hgnc_id": 26234,
"hgvs_c": "c.-295-3208T>G",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 2,
"transcript": "ENST00000969859.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5,BP4",
"acmg_score": 2,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.1715,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.22,
"chr": "17",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Hyperphosphatasia with intellectual disability syndrome 5",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.3215881586074829,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 504,
"aa_ref": "T",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2816,
"cdna_start": 825,
"cds_end": null,
"cds_length": 1515,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001346754.2",
"gene_hgnc_id": 23213,
"gene_symbol": "PIGW",
"hgvs_c": "c.211A>C",
"hgvs_p": "p.Thr71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000614443.2",
"protein_coding": true,
"protein_id": "NP_001333683.1",
"strand": true,
"transcript": "NM_001346754.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 504,
"aa_ref": "T",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2816,
"cdna_start": 825,
"cds_end": null,
"cds_length": 1515,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000614443.2",
"gene_hgnc_id": 23213,
"gene_symbol": "PIGW",
"hgvs_c": "c.211A>C",
"hgvs_p": "p.Thr71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001346754.2",
"protein_coding": true,
"protein_id": "ENSP00000482202.1",
"strand": true,
"transcript": "ENST00000614443.2",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 276,
"aa_ref": "T",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 876,
"cdna_start": 254,
"cds_end": null,
"cds_length": 833,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000619326.1",
"gene_hgnc_id": 23213,
"gene_symbol": "PIGW",
"hgvs_c": "c.211A>C",
"hgvs_p": "p.Thr71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000480475.1",
"strand": true,
"transcript": "ENST00000619326.1",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 504,
"aa_ref": "T",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2278,
"cdna_start": 287,
"cds_end": null,
"cds_length": 1515,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001346755.2",
"gene_hgnc_id": 23213,
"gene_symbol": "PIGW",
"hgvs_c": "c.211A>C",
"hgvs_p": "p.Thr71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001333684.1",
"strand": true,
"transcript": "NM_001346755.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 504,
"aa_ref": "T",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2825,
"cdna_start": 834,
"cds_end": null,
"cds_length": 1515,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_178517.5",
"gene_hgnc_id": 23213,
"gene_symbol": "PIGW",
"hgvs_c": "c.211A>C",
"hgvs_p": "p.Thr71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_848612.2",
"strand": true,
"transcript": "NM_178517.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 504,
"aa_ref": "T",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2264,
"cdna_start": 266,
"cds_end": null,
"cds_length": 1515,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000620233.1",
"gene_hgnc_id": 23213,
"gene_symbol": "PIGW",
"hgvs_c": "c.211A>C",
"hgvs_p": "p.Thr71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000480021.1",
"strand": true,
"transcript": "ENST00000620233.1",
"transcript_support_level": 2
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 504,
"aa_ref": "T",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2302,
"cdna_start": 333,
"cds_end": null,
"cds_length": 1515,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000938181.1",
"gene_hgnc_id": 23213,
"gene_symbol": "PIGW",
"hgvs_c": "c.211A>C",
"hgvs_p": "p.Thr71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608240.1",
"strand": true,
"transcript": "ENST00000938181.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 970,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4104,
"cdna_start": null,
"cds_end": null,
"cds_length": 2913,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000969859.1",
"gene_hgnc_id": 26234,
"gene_symbol": "MYO19",
"hgvs_c": "c.-295-3208T>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639918.1",
"strand": false,
"transcript": "ENST00000969859.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1047,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5829,
"cdna_start": null,
"cds_end": null,
"cds_length": 3144,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047436823.1",
"gene_hgnc_id": 26234,
"gene_symbol": "MYO19",
"hgvs_c": "c.-295-3208T>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292779.1",
"strand": false,
"transcript": "XM_047436823.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 578,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000610496.1",
"gene_hgnc_id": 26234,
"gene_symbol": "MYO19",
"hgvs_c": "n.396-3208T>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000610496.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 545,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000617167.1",
"gene_hgnc_id": 26234,
"gene_symbol": "MYO19",
"hgvs_c": "n.164-1679T>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000617167.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs587777733",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 23213,
"gene_symbol": "PIGW",
"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": "Pathogenic",
"phenotype_combined": "Hyperphosphatasia with intellectual disability syndrome 5",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.029,
"pos": 36537312,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.284,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_178517.5"
}
]
}