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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: 9-110304489-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=110304489&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "TXNDC8",
"hgnc_id": 31454,
"hgvs_c": "c.299G>T",
"hgvs_p": "p.Arg100Ile",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_001424031.1",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000302400",
"hgnc_id": null,
"hgvs_c": "n.581-7832C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "ENST00000786399.1",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC124902246",
"hgnc_id": null,
"hgvs_c": "n.806-7832C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": 0,
"transcript": "XR_007061729.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 25,
"alphamissense_prediction": null,
"alphamissense_score": 0.2086,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "9",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.586712658405304,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 127,
"aa_ref": "R",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 496,
"cdna_start": 366,
"cds_end": null,
"cds_length": 384,
"cds_start": 299,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001424031.1",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.299G>T",
"hgvs_p": "p.Arg100Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374511.8",
"protein_coding": true,
"protein_id": "NP_001410960.1",
"strand": false,
"transcript": "NM_001424031.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 127,
"aa_ref": "R",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 496,
"cdna_start": 366,
"cds_end": null,
"cds_length": 384,
"cds_start": 299,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000374511.8",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.299G>T",
"hgvs_p": "p.Arg100Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001424031.1",
"protein_coding": true,
"protein_id": "ENSP00000363635.3",
"strand": false,
"transcript": "ENST00000374511.8",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 115,
"aa_ref": "R",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 455,
"cdna_start": 311,
"cds_end": null,
"cds_length": 348,
"cds_start": 299,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000374510.8",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.299G>T",
"hgvs_p": "p.Arg100Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363634.4",
"strand": false,
"transcript": "ENST00000374510.8",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 95,
"aa_ref": "R",
"aa_start": 80,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 561,
"cdna_start": 306,
"cds_end": null,
"cds_length": 288,
"cds_start": 239,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000423740.7",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.239G>T",
"hgvs_p": "p.Arg80Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000408768.2",
"strand": false,
"transcript": "ENST00000423740.7",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 120,
"aa_ref": "R",
"aa_start": 93,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 450,
"cdna_start": 320,
"cds_end": null,
"cds_length": 363,
"cds_start": 278,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000713585.1",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.278G>T",
"hgvs_p": "p.Arg93Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000518877.1",
"strand": false,
"transcript": "ENST00000713585.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 115,
"aa_ref": "R",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 621,
"cdna_start": 366,
"cds_end": null,
"cds_length": 348,
"cds_start": 299,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001003936.4",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.299G>T",
"hgvs_p": "p.Arg100Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001003936.1",
"strand": false,
"transcript": "NM_001003936.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 95,
"aa_ref": "R",
"aa_start": 80,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 561,
"cdna_start": 306,
"cds_end": null,
"cds_length": 288,
"cds_start": 239,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001286946.2",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.239G>T",
"hgvs_p": "p.Arg80Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001273875.1",
"strand": false,
"transcript": "NM_001286946.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 138,
"aa_ref": "R",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 524,
"cdna_start": 366,
"cds_end": null,
"cds_length": 417,
"cds_start": 299,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017014579.2",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.299G>T",
"hgvs_p": "p.Arg100Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016870068.1",
"strand": false,
"transcript": "XM_017014579.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 118,
"aa_ref": "R",
"aa_start": 80,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 464,
"cdna_start": 306,
"cds_end": null,
"cds_length": 357,
"cds_start": 239,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017014582.2",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.239G>T",
"hgvs_p": "p.Arg80Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016870071.1",
"strand": false,
"transcript": "XM_017014582.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 101,
"aa_ref": "R",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 514,
"cdna_start": 356,
"cds_end": null,
"cds_length": 306,
"cds_start": 188,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017014584.2",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.188G>T",
"hgvs_p": "p.Arg63Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016870073.1",
"strand": false,
"transcript": "XM_017014584.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 105,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 430,
"cdna_start": null,
"cds_end": null,
"cds_length": 318,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001364963.2",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.256-906G>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001351892.1",
"strand": false,
"transcript": "NM_001364963.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 105,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 458,
"cdna_start": null,
"cds_end": null,
"cds_length": 318,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000713575.1",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.256-906G>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000518867.1",
"strand": false,
"transcript": "ENST00000713575.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 116,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 458,
"cdna_start": null,
"cds_end": null,
"cds_length": 351,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017014583.2",
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"hgvs_c": "c.256-906G>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016870072.1",
"strand": false,
"transcript": "XM_017014583.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 914,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000786399.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000302400",
"hgvs_c": "n.581-7832C>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000786399.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 616,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000786400.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000302400",
"hgvs_c": "n.437-7832C>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000786400.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 924,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000786401.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000302400",
"hgvs_c": "n.504-7832C>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000786401.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 368,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000786402.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000302400",
"hgvs_c": "n.254-7832C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000786402.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 680,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000786403.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000302400",
"hgvs_c": "n.575-7832C>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000786403.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 920,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007061729.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC124902246",
"hgvs_c": "n.806-7832C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007061729.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs200278329",
"effect": "missense_variant",
"frequency_reference_population": 0.000015524769,
"gene_hgnc_id": 31454,
"gene_symbol": "TXNDC8",
"gnomad_exomes_ac": 20,
"gnomad_exomes_af": 0.0000137164,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328476,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.805,
"pos": 110304489,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.212,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001424031.1"
}
]
}