← Back to variant description
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: 10-87727289-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=87727289&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PAPSS2",
"hgnc_id": 8604,
"hgvs_c": "c.886G>A",
"hgvs_p": "p.Val296Met",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_001015880.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 19288,
"alphamissense_prediction": null,
"alphamissense_score": 0.0971,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "10",
"clinvar_classification": "Benign",
"clinvar_disease": " PAPSS2 type,Spondyloepimetaphyseal dysplasia,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.008572250604629517,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 619,
"aa_ref": "V",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3699,
"cdna_start": 990,
"cds_end": null,
"cds_length": 1860,
"cds_start": 886,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001015880.2",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.886G>A",
"hgvs_p": "p.Val296Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000456849.2",
"protein_coding": true,
"protein_id": "NP_001015880.1",
"strand": true,
"transcript": "NM_001015880.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 619,
"aa_ref": "V",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3699,
"cdna_start": 990,
"cds_end": null,
"cds_length": 1860,
"cds_start": 886,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000456849.2",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.886G>A",
"hgvs_p": "p.Val296Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001015880.2",
"protein_coding": true,
"protein_id": "ENSP00000406157.1",
"strand": true,
"transcript": "ENST00000456849.2",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 614,
"aa_ref": "V",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3949,
"cdna_start": 1240,
"cds_end": null,
"cds_length": 1845,
"cds_start": 871,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000361175.8",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.871G>A",
"hgvs_p": "p.Val291Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000354436.4",
"strand": true,
"transcript": "ENST00000361175.8",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 637,
"aa_ref": "V",
"aa_start": 314,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4010,
"cdna_start": 1298,
"cds_end": null,
"cds_length": 1914,
"cds_start": 940,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000904622.1",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.940G>A",
"hgvs_p": "p.Val314Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574681.1",
"strand": true,
"transcript": "ENST00000904622.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 631,
"aa_ref": "V",
"aa_start": 314,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3732,
"cdna_start": 1044,
"cds_end": null,
"cds_length": 1896,
"cds_start": 940,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000904623.1",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.940G>A",
"hgvs_p": "p.Val314Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574682.1",
"strand": true,
"transcript": "ENST00000904623.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 614,
"aa_ref": "V",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3684,
"cdna_start": 975,
"cds_end": null,
"cds_length": 1845,
"cds_start": 871,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_004670.4",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.871G>A",
"hgvs_p": "p.Val291Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_004661.2",
"strand": true,
"transcript": "NM_004670.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 613,
"aa_ref": "V",
"aa_start": 296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2404,
"cdna_start": 1015,
"cds_end": null,
"cds_length": 1842,
"cds_start": 886,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000947767.1",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.886G>A",
"hgvs_p": "p.Val296Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617826.1",
"strand": true,
"transcript": "ENST00000947767.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 612,
"aa_ref": "V",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3165,
"cdna_start": 971,
"cds_end": null,
"cds_length": 1839,
"cds_start": 871,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000904625.1",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.871G>A",
"hgvs_p": "p.Val291Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574684.1",
"strand": true,
"transcript": "ENST00000904625.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 603,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3127,
"cdna_start": null,
"cds_end": null,
"cds_length": 1812,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000947766.1",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.881-43G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617825.1",
"strand": true,
"transcript": "ENST00000947766.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 598,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3818,
"cdna_start": null,
"cds_end": null,
"cds_length": 1797,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000928413.1",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.866-43G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000598472.1",
"strand": true,
"transcript": "ENST00000928413.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 266,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2184,
"cdna_start": null,
"cds_end": null,
"cds_length": 801,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000904624.1",
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"hgvs_c": "c.28-13946G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574683.1",
"strand": true,
"transcript": "ENST00000904624.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs45467596",
"effect": "missense_variant",
"frequency_reference_population": 0.011959236,
"gene_hgnc_id": 8604,
"gene_symbol": "PAPSS2",
"gnomad_exomes_ac": 18002,
"gnomad_exomes_af": 0.0123256,
"gnomad_exomes_homalt": 136,
"gnomad_genomes_ac": 1286,
"gnomad_genomes_af": 0.00844508,
"gnomad_genomes_homalt": 5,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 141,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Spondyloepimetaphyseal dysplasia, PAPSS2 type|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.125,
"pos": 87727289,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.056,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_001015880.2"
}
]
}