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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: 10-87745165-TCATTC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=87745165&ref=TCATTC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 87745165,
"ref": "TCATTC",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "NM_001015880.2",
"consequences": [
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1662_1666delATTCC",
"hgvs_p": "p.Phe555fs",
"transcript": "NM_001015880.2",
"protein_id": "NP_001015880.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 619,
"cds_start": 1662,
"cds_end": null,
"cds_length": 1860,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000456849.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001015880.2"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1662_1666delATTCC",
"hgvs_p": "p.Phe555fs",
"transcript": "ENST00000456849.2",
"protein_id": "ENSP00000406157.1",
"transcript_support_level": 1,
"aa_start": 554,
"aa_end": null,
"aa_length": 619,
"cds_start": 1662,
"cds_end": null,
"cds_length": 1860,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001015880.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000456849.2"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1647_1651delATTCC",
"hgvs_p": "p.Phe550fs",
"transcript": "ENST00000361175.8",
"protein_id": "ENSP00000354436.4",
"transcript_support_level": 1,
"aa_start": 549,
"aa_end": null,
"aa_length": 614,
"cds_start": 1647,
"cds_end": null,
"cds_length": 1845,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361175.8"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1716_1720delATTCC",
"hgvs_p": "p.Phe573fs",
"transcript": "ENST00000904622.1",
"protein_id": "ENSP00000574681.1",
"transcript_support_level": null,
"aa_start": 572,
"aa_end": null,
"aa_length": 637,
"cds_start": 1716,
"cds_end": null,
"cds_length": 1914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904622.1"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1698_1702delATTCC",
"hgvs_p": "p.Phe567fs",
"transcript": "ENST00000904623.1",
"protein_id": "ENSP00000574682.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 631,
"cds_start": 1698,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904623.1"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1647_1651delATTCC",
"hgvs_p": "p.Phe550fs",
"transcript": "NM_004670.4",
"protein_id": "NP_004661.2",
"transcript_support_level": null,
"aa_start": 549,
"aa_end": null,
"aa_length": 614,
"cds_start": 1647,
"cds_end": null,
"cds_length": 1845,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004670.4"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1644_1648delATTCC",
"hgvs_p": "p.Phe549fs",
"transcript": "ENST00000947767.1",
"protein_id": "ENSP00000617826.1",
"transcript_support_level": null,
"aa_start": 548,
"aa_end": null,
"aa_length": 613,
"cds_start": 1644,
"cds_end": null,
"cds_length": 1842,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947767.1"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1641_1645delATTCC",
"hgvs_p": "p.Phe548fs",
"transcript": "ENST00000904625.1",
"protein_id": "ENSP00000574684.1",
"transcript_support_level": null,
"aa_start": 547,
"aa_end": null,
"aa_length": 612,
"cds_start": 1641,
"cds_end": null,
"cds_length": 1839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904625.1"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1614_1618delATTCC",
"hgvs_p": "p.Phe539fs",
"transcript": "ENST00000947766.1",
"protein_id": "ENSP00000617825.1",
"transcript_support_level": null,
"aa_start": 538,
"aa_end": null,
"aa_length": 603,
"cds_start": 1614,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947766.1"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.1599_1603delATTCC",
"hgvs_p": "p.Phe534fs",
"transcript": "ENST00000928413.1",
"protein_id": "ENSP00000598472.1",
"transcript_support_level": null,
"aa_start": 533,
"aa_end": null,
"aa_length": 598,
"cds_start": 1599,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928413.1"
},
{
"aa_ref": "PFR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"hgvs_c": "c.603_607delATTCC",
"hgvs_p": "p.Phe202fs",
"transcript": "ENST00000904624.1",
"protein_id": "ENSP00000574683.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 266,
"cds_start": 603,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904624.1"
}
],
"gene_symbol": "PAPSS2",
"gene_hgnc_id": 8604,
"dbsnp": "rs797045099",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.669,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_001015880.2",
"gene_symbol": "PAPSS2",
"hgnc_id": 8604,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1662_1666delATTCC",
"hgvs_p": "p.Phe555fs"
}
],
"clinvar_disease": " PAPSS2 type,Spondyloepimetaphyseal dysplasia",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Spondyloepimetaphyseal dysplasia, PAPSS2 type",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}