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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: 17-4533107-CC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4533107&ref=CC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 4533107,
"ref": "CC",
"alt": "T",
"effect": "frameshift_variant,missense_variant",
"transcript": "NM_001124758.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "c.1066_1067delCCinsT",
"hgvs_p": "p.Pro356fs",
"transcript": "NM_001124758.3",
"protein_id": "NP_001118230.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 549,
"cds_start": 1066,
"cds_end": null,
"cds_length": 1650,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 3404,
"mane_select": "ENST00000329078.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001124758.3"
},
{
"aa_ref": "P",
"aa_alt": "?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "c.1066_1067delCCinsT",
"hgvs_p": "p.Pro356fs",
"transcript": "ENST00000329078.8",
"protein_id": "ENSP00000333292.3",
"transcript_support_level": 1,
"aa_start": 356,
"aa_end": null,
"aa_length": 549,
"cds_start": 1066,
"cds_end": null,
"cds_length": 1650,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 3404,
"mane_select": "NM_001124758.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000329078.8"
},
{
"aa_ref": "P",
"aa_alt": "?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "c.1060_1061delCCinsT",
"hgvs_p": "p.Pro354fs",
"transcript": "ENST00000947403.1",
"protein_id": "ENSP00000617462.1",
"transcript_support_level": null,
"aa_start": 354,
"aa_end": null,
"aa_length": 547,
"cds_start": 1060,
"cds_end": null,
"cds_length": 1644,
"cdna_start": 1226,
"cdna_end": null,
"cdna_length": 3397,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947403.1"
},
{
"aa_ref": "P",
"aa_alt": "?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "c.1000_1001delCCinsT",
"hgvs_p": "p.Pro334fs",
"transcript": "ENST00000932033.1",
"protein_id": "ENSP00000602092.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 527,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1178,
"cdna_end": null,
"cdna_length": 3350,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932033.1"
},
{
"aa_ref": "P",
"aa_alt": "?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "c.1066_1067delCCinsT",
"hgvs_p": "p.Pro356fs",
"transcript": "ENST00000947402.1",
"protein_id": "ENSP00000617461.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 527,
"cds_start": 1066,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 3370,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947402.1"
},
{
"aa_ref": "P",
"aa_alt": "?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "c.76_77delCCinsT",
"hgvs_p": "p.Pro26fs",
"transcript": "ENST00000571386.1",
"protein_id": "ENSP00000461410.1",
"transcript_support_level": 5,
"aa_start": 26,
"aa_end": null,
"aa_length": 281,
"cds_start": 76,
"cds_end": null,
"cds_length": 846,
"cdna_start": 76,
"cdna_end": null,
"cdna_length": 846,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000571386.1"
},
{
"aa_ref": "P",
"aa_alt": "?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "c.613_614delCCinsT",
"hgvs_p": "p.Pro205fs",
"transcript": "XM_047435339.1",
"protein_id": "XP_047291295.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 398,
"cds_start": 613,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 927,
"cdna_end": null,
"cdna_length": 3098,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047435339.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "n.1233_1234delCCinsT",
"hgvs_p": null,
"transcript": "XR_007065260.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3518,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007065260.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "n.903_904delCCinsT",
"hgvs_p": null,
"transcript": "XR_007065261.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3188,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007065261.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"hgvs_c": "n.-136_-135delCCinsT",
"hgvs_p": null,
"transcript": "ENST00000576635.6",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 901,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000576635.6"
}
],
"gene_symbol": "SPNS2",
"gene_hgnc_id": 26992,
"dbsnp": "rs1555537637",
"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": 1.826,
"phylop100way_prediction": "Benign",
"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_001124758.3",
"gene_symbol": "SPNS2",
"hgnc_id": 26992,
"effects": [
"frameshift_variant",
"missense_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.1066_1067delCCinsT",
"hgvs_p": "p.Pro356fs"
}
],
"clinvar_disease": " autosomal recessive 115,Hearing loss,Inborn genetic diseases",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "Inborn genetic diseases|Hearing loss, autosomal recessive 115",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}