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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: 12-120768381-GG-AT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=120768381&ref=GG&alt=AT&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SPPL3",
"hgnc_id": 30424,
"hgvs_c": "c.716_717delCCinsAT",
"hgvs_p": "p.Pro239His",
"inheritance_mode": "",
"pathogenic_score": 1,
"score": 1,
"transcript": "NM_139015.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_score": 1,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "AT",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "12",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 384,
"aa_ref": "P",
"aa_start": 239,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4135,
"cdna_start": 1208,
"cds_end": null,
"cds_length": 1155,
"cds_start": 716,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_139015.5",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.716_717delCCinsAT",
"hgvs_p": "p.Pro239His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000353487.7",
"protein_coding": true,
"protein_id": "NP_620584.2",
"strand": false,
"transcript": "NM_139015.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 384,
"aa_ref": "P",
"aa_start": 239,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4135,
"cdna_start": 1208,
"cds_end": null,
"cds_length": 1155,
"cds_start": 716,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000353487.7",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.716_717delCCinsAT",
"hgvs_p": "p.Pro239His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_139015.5",
"protein_coding": true,
"protein_id": "ENSP00000288680.4",
"strand": false,
"transcript": "ENST00000353487.7",
"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": 797,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000545209.1",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "n.250_251delCCinsAT",
"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": "ENST00000545209.1",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 380,
"aa_ref": "P",
"aa_start": 239,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1991,
"cdna_start": 1027,
"cds_end": null,
"cds_length": 1143,
"cds_start": 716,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000961961.1",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.716_717delCCinsAT",
"hgvs_p": "p.Pro239His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632020.1",
"strand": false,
"transcript": "ENST00000961961.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 358,
"aa_ref": "P",
"aa_start": 213,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2742,
"cdna_start": 1128,
"cds_end": null,
"cds_length": 1077,
"cds_start": 638,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000855477.1",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.638_639delCCinsAT",
"hgvs_p": "p.Pro213His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525536.1",
"strand": false,
"transcript": "ENST00000855477.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 344,
"aa_ref": "P",
"aa_start": 199,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2728,
"cdna_start": 1086,
"cds_end": null,
"cds_length": 1035,
"cds_start": 596,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000913320.1",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.596_597delCCinsAT",
"hgvs_p": "p.Pro199His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583379.1",
"strand": false,
"transcript": "ENST00000913320.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 344,
"aa_ref": "P",
"aa_start": 199,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2617,
"cdna_start": 989,
"cds_end": null,
"cds_length": 1035,
"cds_start": 596,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000961959.1",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.596_597delCCinsAT",
"hgvs_p": "p.Pro199His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632018.1",
"strand": false,
"transcript": "ENST00000961959.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 320,
"aa_ref": "P",
"aa_start": 175,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1979,
"cdna_start": 817,
"cds_end": null,
"cds_length": 963,
"cds_start": 524,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000961960.1",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.524_525delCCinsAT",
"hgvs_p": "p.Pro175His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632019.1",
"strand": false,
"transcript": "ENST00000961960.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 280,
"aa_ref": "P",
"aa_start": 135,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1768,
"cdna_start": 604,
"cds_end": null,
"cds_length": 843,
"cds_start": 404,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000855478.1",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.404_405delCCinsAT",
"hgvs_p": "p.Pro135His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525537.1",
"strand": false,
"transcript": "ENST00000855478.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 384,
"aa_ref": "P",
"aa_start": 239,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 38708,
"cdna_start": 35781,
"cds_end": null,
"cds_length": 1155,
"cds_start": 716,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011537925.3",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.716_717delCCinsAT",
"hgvs_p": "p.Pro239His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536227.1",
"strand": false,
"transcript": "XM_011537925.3",
"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": 2265,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000392495.7",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "n.1292_1293delCCinsAT",
"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": "ENST00000392495.7",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 182,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 763,
"cdna_start": null,
"cds_end": null,
"cds_length": 549,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000536996.5",
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"hgvs_c": "c.*56_*57delCCinsAT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000442484.1",
"strand": true,
"transcript": "ENST00000536996.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 30424,
"gene_symbol": "SPPL3",
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"pos": 120768381,
"ref": "GG",
"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_139015.5"
}
]
}