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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: 3-57106133-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=57106133&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "IL17RD",
"hgnc_id": 17616,
"hgvs_c": "c.572C>T",
"hgvs_p": "p.Pro191Leu",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_017563.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 217,
"alphamissense_prediction": null,
"alphamissense_score": 0.1928,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.32,
"chr": "3",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Cerebral arteriovenous malformation,Delayed puberty,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:2 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.13986924290657043,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 739,
"aa_ref": "P",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8698,
"cdna_start": 639,
"cds_end": null,
"cds_length": 2220,
"cds_start": 572,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_017563.5",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.572C>T",
"hgvs_p": "p.Pro191Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000296318.12",
"protein_coding": true,
"protein_id": "NP_060033.3",
"strand": false,
"transcript": "NM_017563.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 739,
"aa_ref": "P",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8698,
"cdna_start": 639,
"cds_end": null,
"cds_length": 2220,
"cds_start": 572,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000296318.12",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.572C>T",
"hgvs_p": "p.Pro191Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017563.5",
"protein_coding": true,
"protein_id": "ENSP00000296318.7",
"strand": false,
"transcript": "ENST00000296318.12",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 595,
"aa_ref": "P",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4474,
"cdna_start": 683,
"cds_end": null,
"cds_length": 1788,
"cds_start": 140,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000320057.9",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.140C>T",
"hgvs_p": "p.Pro47Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000322250.5",
"strand": false,
"transcript": "ENST00000320057.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 595,
"aa_ref": "P",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2348,
"cdna_start": 485,
"cds_end": null,
"cds_length": 1788,
"cds_start": 140,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000463523.5",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.140C>T",
"hgvs_p": "p.Pro47Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417516.1",
"strand": false,
"transcript": "ENST00000463523.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 732,
"aa_ref": "P",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8673,
"cdna_start": 635,
"cds_end": null,
"cds_length": 2199,
"cds_start": 572,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000914043.1",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.572C>T",
"hgvs_p": "p.Pro191Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584102.1",
"strand": false,
"transcript": "ENST00000914043.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 702,
"aa_ref": "P",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8580,
"cdna_start": 635,
"cds_end": null,
"cds_length": 2109,
"cds_start": 572,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000914044.1",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.572C>T",
"hgvs_p": "p.Pro191Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584103.1",
"strand": false,
"transcript": "ENST00000914044.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 653,
"aa_ref": "P",
"aa_start": 149,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4135,
"cdna_start": 474,
"cds_end": null,
"cds_length": 1962,
"cds_start": 446,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000914045.1",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.446C>T",
"hgvs_p": "p.Pro149Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584104.1",
"strand": false,
"transcript": "ENST00000914045.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 595,
"aa_ref": "P",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8753,
"cdna_start": 694,
"cds_end": null,
"cds_length": 1788,
"cds_start": 140,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001318864.2",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.140C>T",
"hgvs_p": "p.Pro47Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305793.1",
"strand": false,
"transcript": "NM_001318864.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 72,
"aa_ref": "P",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 589,
"cdna_start": 509,
"cds_end": null,
"cds_length": 220,
"cds_start": 140,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000467210.5",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.140C>T",
"hgvs_p": "p.Pro47Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418368.1",
"strand": false,
"transcript": "ENST00000467210.5",
"transcript_support_level": 4
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 711,
"aa_ref": "P",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8933,
"cdna_start": 874,
"cds_end": null,
"cds_length": 2136,
"cds_start": 488,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_005265238.5",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.488C>T",
"hgvs_p": "p.Pro163Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005265295.1",
"strand": false,
"transcript": "XM_005265238.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 595,
"aa_ref": "P",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8539,
"cdna_start": 480,
"cds_end": null,
"cds_length": 1788,
"cds_start": 140,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_011533849.2",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.140C>T",
"hgvs_p": "p.Pro47Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532151.2",
"strand": false,
"transcript": "XM_011533849.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 595,
"aa_ref": "P",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8835,
"cdna_start": 776,
"cds_end": null,
"cds_length": 1788,
"cds_start": 140,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047448369.1",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "c.140C>T",
"hgvs_p": "p.Pro47Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304325.1",
"strand": false,
"transcript": "XM_047448369.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2167,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000469841.5",
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"hgvs_c": "n.509C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000469841.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs200088377",
"effect": "missense_variant",
"frequency_reference_population": 0.00013461588,
"gene_hgnc_id": 17616,
"gene_symbol": "IL17RD",
"gnomad_exomes_ac": 195,
"gnomad_exomes_af": 0.000133566,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 22,
"gnomad_genomes_af": 0.000144695,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Delayed puberty|Cerebral arteriovenous malformation|not specified|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.519,
"pos": 57106133,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.302,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_017563.5"
}
]
}