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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: 3-121772575-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=121772575&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 121772575,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000310864.11",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.1549A>G",
"hgvs_p": "p.Asn517Asp",
"transcript": "NM_001023570.4",
"protein_id": "NP_001018864.2",
"transcript_support_level": null,
"aa_start": 517,
"aa_end": null,
"aa_length": 598,
"cds_start": 1549,
"cds_end": null,
"cds_length": 1797,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 2577,
"mane_select": "ENST00000310864.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.1549A>G",
"hgvs_p": "p.Asn517Asp",
"transcript": "ENST00000310864.11",
"protein_id": "ENSP00000311505.6",
"transcript_support_level": 1,
"aa_start": 517,
"aa_end": null,
"aa_length": 598,
"cds_start": 1549,
"cds_end": null,
"cds_length": 1797,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 2577,
"mane_select": "NM_001023570.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.1150A>G",
"hgvs_p": "p.Asn384Asp",
"transcript": "ENST00000349820.10",
"protein_id": "ENSP00000323756.7",
"transcript_support_level": 1,
"aa_start": 384,
"aa_end": null,
"aa_length": 465,
"cds_start": 1150,
"cds_end": null,
"cds_length": 1398,
"cdna_start": 1320,
"cdna_end": null,
"cdna_length": 1919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.1549A>G",
"hgvs_p": "p.Asn517Asp",
"transcript": "NM_001319107.2",
"protein_id": "NP_001306036.1",
"transcript_support_level": null,
"aa_start": 517,
"aa_end": null,
"aa_length": 598,
"cds_start": 1549,
"cds_end": null,
"cds_length": 1797,
"cdna_start": 1744,
"cdna_end": null,
"cdna_length": 2576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.1150A>G",
"hgvs_p": "p.Asn384Asp",
"transcript": "NM_001023571.4",
"protein_id": "NP_001018865.2",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 465,
"cds_start": 1150,
"cds_end": null,
"cds_length": 1398,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 2178,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.997A>G",
"hgvs_p": "p.Asn333Asp",
"transcript": "XM_047449250.1",
"protein_id": "XP_047305206.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 414,
"cds_start": 997,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 1377,
"cdna_end": null,
"cdna_length": 2209,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.997A>G",
"hgvs_p": "p.Asn333Asp",
"transcript": "XM_047449251.1",
"protein_id": "XP_047305207.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 414,
"cds_start": 997,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 1283,
"cdna_end": null,
"cdna_length": 2115,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "n.*527A>G",
"hgvs_p": null,
"transcript": "ENST00000393650.7",
"protein_id": "ENSP00000377261.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "n.1634A>G",
"hgvs_p": null,
"transcript": "NR_134968.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "n.*527A>G",
"hgvs_p": null,
"transcript": "ENST00000393650.7",
"protein_id": "ENSP00000377261.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.1411-2001A>G",
"hgvs_p": null,
"transcript": "XM_005247911.5",
"protein_id": "XP_005247968.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 474,
"cds_start": -4,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"hgvs_c": "c.1012-2001A>G",
"hgvs_p": null,
"transcript": "XM_017007539.3",
"protein_id": "XP_016863028.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 341,
"cds_start": -4,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IQCB1",
"gene_hgnc_id": 28949,
"dbsnp": "rs139468837",
"frequency_reference_population": 0.00001313836,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131384,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15485727787017822,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.232,
"revel_prediction": "Benign",
"alphamissense_score": 0.0995,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.896,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000310864.11",
"gene_symbol": "IQCB1",
"hgnc_id": 28949,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1549A>G",
"hgvs_p": "p.Asn517Asp"
}
],
"clinvar_disease": "Nephronophthisis",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Nephronophthisis",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}