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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: 3-48467117-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=48467117&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 48467117,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000625293.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"hgvs_c": "c.462T>C",
"hgvs_p": "p.Asp154Asp",
"transcript": "NM_033629.6",
"protein_id": "NP_338599.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 314,
"cds_start": 462,
"cds_end": null,
"cds_length": 945,
"cdna_start": 568,
"cdna_end": null,
"cdna_length": 1096,
"mane_select": "ENST00000625293.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"hgvs_c": "c.462T>C",
"hgvs_p": "p.Asp154Asp",
"transcript": "ENST00000625293.3",
"protein_id": "ENSP00000486676.2",
"transcript_support_level": 6,
"aa_start": 154,
"aa_end": null,
"aa_length": 314,
"cds_start": 462,
"cds_end": null,
"cds_length": 945,
"cdna_start": 568,
"cdna_end": null,
"cdna_length": 1096,
"mane_select": "NM_033629.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"hgvs_c": "c.432T>C",
"hgvs_p": "p.Asp144Asp",
"transcript": "ENST00000444177.1",
"protein_id": "ENSP00000415972.1",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 304,
"cds_start": 432,
"cds_end": null,
"cds_length": 915,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 1200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"hgvs_c": "c.45T>C",
"hgvs_p": "p.Asp15Asp",
"transcript": "ENST00000433541.1",
"protein_id": "ENSP00000412404.1",
"transcript_support_level": 1,
"aa_start": 15,
"aa_end": null,
"aa_length": 175,
"cds_start": 45,
"cds_end": null,
"cds_length": 528,
"cdna_start": 577,
"cdna_end": null,
"cdna_length": 1105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "c.*1563T>C",
"hgvs_p": null,
"transcript": "NM_130384.3",
"protein_id": "NP_569055.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 791,
"cds_start": -4,
"cds_end": null,
"cds_length": 2376,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4576,
"mane_select": "ENST00000320211.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "c.*1563T>C",
"hgvs_p": null,
"transcript": "ENST00000320211.10",
"protein_id": "ENSP00000323099.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 791,
"cds_start": -4,
"cds_end": null,
"cds_length": 2376,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4576,
"mane_select": "NM_130384.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"hgvs_c": "c.432T>C",
"hgvs_p": "p.Asp144Asp",
"transcript": "NM_007248.5",
"protein_id": "NP_009179.2",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 304,
"cds_start": 432,
"cds_end": null,
"cds_length": 915,
"cdna_start": 790,
"cdna_end": null,
"cdna_length": 1318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"hgvs_c": "c.45T>C",
"hgvs_p": "p.Asp15Asp",
"transcript": "ENST00000456089.1",
"protein_id": "ENSP00000411331.1",
"transcript_support_level": 3,
"aa_start": 15,
"aa_end": null,
"aa_length": 175,
"cds_start": 45,
"cds_end": null,
"cds_length": 528,
"cdna_start": 101,
"cdna_end": null,
"cdna_length": 629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"hgvs_c": "c.45T>C",
"hgvs_p": "p.Asp15Asp",
"transcript": "ENST00000492235.2",
"protein_id": "ENSP00000494511.1",
"transcript_support_level": 3,
"aa_start": 15,
"aa_end": null,
"aa_length": 175,
"cds_start": 45,
"cds_end": null,
"cds_length": 528,
"cdna_start": 398,
"cdna_end": null,
"cdna_length": 924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"hgvs_c": "c.45T>C",
"hgvs_p": "p.Asp15Asp",
"transcript": "ENST00000635452.2",
"protein_id": "ENSP00000492023.2",
"transcript_support_level": 2,
"aa_start": 15,
"aa_end": null,
"aa_length": 175,
"cds_start": 45,
"cds_end": null,
"cds_length": 528,
"cdna_start": 431,
"cdna_end": null,
"cdna_length": 958,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "n.*1243T>C",
"hgvs_p": null,
"transcript": "ENST00000634384.2",
"protein_id": "ENSP00000489041.2",
"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": 3585,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "n.*2020T>C",
"hgvs_p": null,
"transcript": "ENST00000635464.1",
"protein_id": "ENSP00000489199.1",
"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": 3943,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP-TREX1",
"gene_hgnc_id": null,
"hgvs_c": "n.3771T>C",
"hgvs_p": null,
"transcript": "NR_153405.1",
"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": 4299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "c.*1563T>C",
"hgvs_p": null,
"transcript": "NM_032166.4",
"protein_id": "NP_115542.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 764,
"cds_start": -4,
"cds_end": null,
"cds_length": 2295,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "c.*1563T>C",
"hgvs_p": null,
"transcript": "NM_001271023.2",
"protein_id": "NP_001257952.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 698,
"cds_start": -4,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4617,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "c.*1563T>C",
"hgvs_p": null,
"transcript": "NM_001271022.2",
"protein_id": "NP_001257951.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 664,
"cds_start": -4,
"cds_end": null,
"cds_length": 1995,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4366,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "n.*1243T>C",
"hgvs_p": null,
"transcript": "ENST00000634384.2",
"protein_id": "ENSP00000489041.2",
"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": 3585,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRIP",
"gene_hgnc_id": 33499,
"hgvs_c": "n.*2020T>C",
"hgvs_p": null,
"transcript": "ENST00000635464.1",
"protein_id": "ENSP00000489199.1",
"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": 3943,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TREX1",
"gene_hgnc_id": 12269,
"dbsnp": "rs3135944",
"frequency_reference_population": 0.0010353891,
"hom_count_reference_population": 16,
"allele_count_reference_population": 1671,
"gnomad_exomes_af": 0.000551423,
"gnomad_genomes_af": 0.00568279,
"gnomad_exomes_ac": 806,
"gnomad_genomes_ac": 865,
"gnomad_exomes_homalt": 10,
"gnomad_genomes_homalt": 6,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6800000071525574,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.009,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000625293.3",
"gene_symbol": "TREX1",
"hgnc_id": 12269,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.462T>C",
"hgvs_p": "p.Asp154Asp"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000320211.10",
"gene_symbol": "ATRIP",
"hgnc_id": 33499,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.*1563T>C",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NR_153405.1",
"gene_symbol": "ATRIP-TREX1",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3771T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Aicardi-Goutieres syndrome 1,Chilblain lupus 1,Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Aicardi-Goutieres syndrome 1|Aicardi-Goutieres syndrome 1;Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations;Chilblain lupus 1|Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations|not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}