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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: 7-139148230-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=139148230&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 139148230,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_024926.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.570T>C",
"hgvs_p": "p.Tyr190Tyr",
"transcript": "NM_024926.4",
"protein_id": "NP_079202.2",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 554,
"cds_start": 570,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 4299,
"mane_select": "ENST00000464848.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.570T>C",
"hgvs_p": "p.Tyr190Tyr",
"transcript": "ENST00000464848.5",
"protein_id": "ENSP00000419279.1",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 554,
"cds_start": 570,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 4299,
"mane_select": "NM_024926.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.570T>C",
"hgvs_p": "p.Tyr190Tyr",
"transcript": "ENST00000430935.5",
"protein_id": "ENSP00000410655.1",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 487,
"cds_start": 570,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 684,
"cdna_end": null,
"cdna_length": 4198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.570T>C",
"hgvs_p": "p.Tyr190Tyr",
"transcript": "ENST00000474035.6",
"protein_id": "ENSP00000443253.1",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 271,
"cds_start": 570,
"cds_end": null,
"cds_length": 816,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 1193,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.399+5925T>C",
"hgvs_p": null,
"transcript": "ENST00000478836.6",
"protein_id": "ENSP00000419178.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 447,
"cds_start": -4,
"cds_end": null,
"cds_length": 1344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.570T>C",
"hgvs_p": "p.Tyr190Tyr",
"transcript": "NM_001321740.2",
"protein_id": "NP_001308669.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 544,
"cds_start": 570,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 4269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.477T>C",
"hgvs_p": "p.Tyr159Tyr",
"transcript": "NM_001144923.3",
"protein_id": "NP_001138395.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 523,
"cds_start": 477,
"cds_end": null,
"cds_length": 1572,
"cdna_start": 557,
"cdna_end": null,
"cdna_length": 4206,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.477T>C",
"hgvs_p": "p.Tyr159Tyr",
"transcript": "ENST00000343187.8",
"protein_id": "ENSP00000339135.4",
"transcript_support_level": 2,
"aa_start": 159,
"aa_end": null,
"aa_length": 523,
"cds_start": 477,
"cds_end": null,
"cds_length": 1572,
"cdna_start": 552,
"cdna_end": null,
"cdna_length": 2015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.570T>C",
"hgvs_p": "p.Tyr190Tyr",
"transcript": "NM_001144920.3",
"protein_id": "NP_001138392.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 487,
"cds_start": 570,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 4165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.255T>C",
"hgvs_p": "p.Tyr85Tyr",
"transcript": "NM_001287513.2",
"protein_id": "NP_001274442.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 449,
"cds_start": 255,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 579,
"cdna_end": null,
"cdna_length": 4228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.150T>C",
"hgvs_p": "p.Tyr50Tyr",
"transcript": "NM_001318333.2",
"protein_id": "NP_001305262.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 414,
"cds_start": 150,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 811,
"cdna_end": null,
"cdna_length": 4460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.570T>C",
"hgvs_p": "p.Tyr190Tyr",
"transcript": "NM_001321742.2",
"protein_id": "NP_001308671.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 271,
"cds_start": 570,
"cds_end": null,
"cds_length": 816,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 1195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "n.535T>C",
"hgvs_p": null,
"transcript": "ENST00000468866.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "n.*323T>C",
"hgvs_p": null,
"transcript": "ENST00000476296.1",
"protein_id": "ENSP00000419639.1",
"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": 2756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "n.648T>C",
"hgvs_p": null,
"transcript": "ENST00000481482.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 1267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "n.*323T>C",
"hgvs_p": null,
"transcript": "ENST00000476296.1",
"protein_id": "ENSP00000419639.1",
"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": 2756,
"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": 16,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.399+5925T>C",
"hgvs_p": null,
"transcript": "NM_001321741.2",
"protein_id": "NP_001308670.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 448,
"cds_start": -4,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3981,
"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": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.399+5925T>C",
"hgvs_p": null,
"transcript": "NM_001287512.2",
"protein_id": "NP_001274441.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 423,
"cds_start": -4,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3906,
"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": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"hgvs_c": "c.399+5925T>C",
"hgvs_p": null,
"transcript": "ENST00000495038.5",
"protein_id": "ENSP00000418788.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 423,
"cds_start": -4,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IFT56",
"gene_hgnc_id": 21882,
"dbsnp": "rs1340170688",
"frequency_reference_population": 0.0000031000138,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000136925,
"gnomad_genomes_af": 0.000019706,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5699999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.001,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_024926.4",
"gene_symbol": "IFT56",
"hgnc_id": 21882,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.570T>C",
"hgvs_p": "p.Tyr190Tyr"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}