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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: 12-125692-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=125692&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 125692,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001170738.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.683C>T",
"hgvs_p": "p.Ala228Val",
"transcript": "NM_001170738.2",
"protein_id": "NP_001164209.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 1182,
"cds_start": 683,
"cds_end": null,
"cds_length": 3549,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 7087,
"mane_select": "ENST00000538872.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.683C>T",
"hgvs_p": "p.Ala228Val",
"transcript": "ENST00000538872.6",
"protein_id": "ENSP00000437554.1",
"transcript_support_level": 5,
"aa_start": 228,
"aa_end": null,
"aa_length": 1182,
"cds_start": 683,
"cds_end": null,
"cds_length": 3549,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 7087,
"mane_select": "NM_001170738.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.683C>T",
"hgvs_p": "p.Ala228Val",
"transcript": "XM_011520958.3",
"protein_id": "XP_011519260.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 1063,
"cds_start": 683,
"cds_end": null,
"cds_length": 3192,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 7070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.683C>T",
"hgvs_p": "p.Ala228Val",
"transcript": "XM_011520960.2",
"protein_id": "XP_011519262.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 1062,
"cds_start": 683,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 3399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.683C>T",
"hgvs_p": "p.Ala228Val",
"transcript": "XM_017019311.2",
"protein_id": "XP_016874800.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 1041,
"cds_start": 683,
"cds_end": null,
"cds_length": 3126,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 3349,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.683C>T",
"hgvs_p": "p.Ala228Val",
"transcript": "XM_047428865.1",
"protein_id": "XP_047284821.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 1041,
"cds_start": 683,
"cds_end": null,
"cds_length": 3126,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 3264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.-6-12575C>T",
"hgvs_p": null,
"transcript": "NM_015232.2",
"protein_id": "NP_056047.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 759,
"cds_start": -4,
"cds_end": null,
"cds_length": 2280,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.-6-12575C>T",
"hgvs_p": null,
"transcript": "ENST00000382841.2",
"protein_id": "ENSP00000372292.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 759,
"cds_start": -4,
"cds_end": null,
"cds_length": 2280,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"hgvs_c": "c.-6-12575C>T",
"hgvs_p": null,
"transcript": "XM_011520961.2",
"protein_id": "XP_011519263.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 879,
"cds_start": -4,
"cds_end": null,
"cds_length": 2640,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IQSEC3",
"gene_hgnc_id": 29193,
"dbsnp": "rs377259498",
"frequency_reference_population": 0.00017232983,
"hom_count_reference_population": 0,
"allele_count_reference_population": 264,
"gnomad_exomes_af": 0.000169613,
"gnomad_genomes_af": 0.000196936,
"gnomad_exomes_ac": 234,
"gnomad_genomes_ac": 30,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05082935094833374,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.192,
"revel_prediction": "Benign",
"alphamissense_score": 0.0892,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.624,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001170738.2",
"gene_symbol": "IQSEC3",
"hgnc_id": 29193,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.683C>T",
"hgvs_p": "p.Ala228Val"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}