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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: 1-145850900-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=145850900&ref=T&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": "PIAS3",
"hgnc_id": 16861,
"hgvs_c": "c.1319A>T",
"hgvs_p": "p.Glu440Val",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_006099.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 37,
"alphamissense_prediction": null,
"alphamissense_score": 0.1187,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.23818647861480713,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 628,
"aa_ref": "E",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2902,
"cdna_start": 1410,
"cds_end": null,
"cds_length": 1887,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_006099.3",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "c.1319A>T",
"hgvs_p": "p.Glu440Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000393045.7",
"protein_coding": true,
"protein_id": "NP_006090.2",
"strand": false,
"transcript": "NM_006099.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 628,
"aa_ref": "E",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2902,
"cdna_start": 1410,
"cds_end": null,
"cds_length": 1887,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000393045.7",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "c.1319A>T",
"hgvs_p": "p.Glu440Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006099.3",
"protein_coding": true,
"protein_id": "ENSP00000376765.2",
"strand": false,
"transcript": "ENST00000393045.7",
"transcript_support_level": 1
},
{
"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": 2679,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000475261.1",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "n.1187A>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": "ENST00000475261.1",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 626,
"aa_ref": "E",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2897,
"cdna_start": 1410,
"cds_end": null,
"cds_length": 1881,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000948928.1",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "c.1319A>T",
"hgvs_p": "p.Glu440Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618987.1",
"strand": false,
"transcript": "ENST00000948928.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 621,
"aa_ref": "E",
"aa_start": 433,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2878,
"cdna_start": 1386,
"cds_end": null,
"cds_length": 1866,
"cds_start": 1298,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000867627.1",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "c.1298A>T",
"hgvs_p": "p.Glu433Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537686.1",
"strand": false,
"transcript": "ENST00000867627.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 609,
"aa_ref": "E",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2845,
"cdna_start": 1353,
"cds_end": null,
"cds_length": 1830,
"cds_start": 1262,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000948929.1",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "c.1262A>T",
"hgvs_p": "p.Glu421Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618988.1",
"strand": false,
"transcript": "ENST00000948929.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 593,
"aa_ref": "E",
"aa_start": 405,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2761,
"cdna_start": 1269,
"cds_end": null,
"cds_length": 1782,
"cds_start": 1214,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000369298.5",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "c.1214A>T",
"hgvs_p": "p.Glu405Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358304.1",
"strand": false,
"transcript": "ENST00000369298.5",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 439,
"aa_ref": "E",
"aa_start": 251,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1415,
"cdna_start": 807,
"cds_end": null,
"cds_length": 1320,
"cds_start": 752,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000867628.1",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "c.752A>T",
"hgvs_p": "p.Glu251Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537687.1",
"strand": false,
"transcript": "ENST00000867628.1",
"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": 2386,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000472114.5",
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"hgvs_c": "n.375A>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": "ENST00000472114.5",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376991349",
"effect": "missense_variant",
"frequency_reference_population": 0.000022923105,
"gene_hgnc_id": 16861,
"gene_symbol": "PIAS3",
"gnomad_exomes_ac": 36,
"gnomad_exomes_af": 0.0000246256,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065703,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.149,
"pos": 145850900,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_006099.3"
}
]
}