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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: 3-45874730-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=45874730&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 45874730,
"ref": "C",
"alt": "A",
"effect": "intron_variant",
"transcript": "NM_001405920.1",
"consequences": [
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.28-36679G>T",
"hgvs_p": null,
"transcript": "NM_001405920.1",
"protein_id": "NP_001392849.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 307,
"cds_start": -4,
"cds_end": null,
"cds_length": 924,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4257,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.28-19656G>T",
"hgvs_p": null,
"transcript": "NM_001405921.1",
"protein_id": "NP_001392850.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 295,
"cds_start": -4,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4221,
"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": 12,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-137-19656G>T",
"hgvs_p": null,
"transcript": "NM_001276378.2",
"protein_id": "NP_001263307.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 282,
"cds_start": -4,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4346,
"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": 13,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-176-15752G>T",
"hgvs_p": null,
"transcript": "NM_001405923.1",
"protein_id": "NP_001392852.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 282,
"cds_start": -4,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4385,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-138+9933G>T",
"hgvs_p": null,
"transcript": "ENST00000684620.1",
"protein_id": "ENSP00000506925.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 282,
"cds_start": -4,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3980,
"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": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.28-36679G>T",
"hgvs_p": null,
"transcript": "NM_001405925.1",
"protein_id": "NP_001392854.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 268,
"cds_start": -4,
"cds_end": null,
"cds_length": 807,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4153,
"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": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.28-19656G>T",
"hgvs_p": null,
"transcript": "NM_001276379.2",
"protein_id": "NP_001263308.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 256,
"cds_start": -4,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
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"cdna_length": 4117,
"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": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.28-19656G>T",
"hgvs_p": null,
"transcript": "ENST00000539217.5",
"protein_id": "ENSP00000441784.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 256,
"cds_start": -4,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4113,
"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": 12,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-176-15752G>T",
"hgvs_p": null,
"transcript": "NM_001405926.1",
"protein_id": "NP_001392855.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 243,
"cds_start": -4,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4281,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-137-19656G>T",
"hgvs_p": null,
"transcript": "NM_001405927.1",
"protein_id": "NP_001392856.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 243,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 4242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-48-36679G>T",
"hgvs_p": null,
"transcript": "ENST00000492333.5",
"protein_id": "ENSP00000505957.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 63,
"cds_start": -4,
"cds_end": null,
"cds_length": 192,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 5,
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"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-214-15714G>T",
"hgvs_p": null,
"transcript": "ENST00000472635.5",
"protein_id": "ENSP00000506465.1",
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},
{
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"strand": false,
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"intron_variant"
],
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"exon_count": 12,
"intron_rank": 2,
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"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "n.28-19656G>T",
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"transcript": "ENST00000418700.6",
"protein_id": "ENSP00000416427.2",
"transcript_support_level": 2,
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},
{
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"protein_coding": false,
"strand": false,
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "n.351-19656G>T",
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"transcript": "ENST00000483279.1",
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 5,
"intron_rank": 2,
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"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "n.402-15752G>T",
"hgvs_p": null,
"transcript": "ENST00000699188.1",
"protein_id": null,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "n.363-15752G>T",
"hgvs_p": null,
"transcript": "NR_170121.1",
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},
{
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],
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"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-12458-19656G>T",
"hgvs_p": null,
"transcript": "XM_047448365.1",
"protein_id": "XP_047304321.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 12,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.-12458-19656G>T",
"hgvs_p": null,
"transcript": "XM_047448366.1",
"protein_id": "XP_047304322.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 12,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"hgvs_c": "c.28-15752G>T",
"hgvs_p": null,
"transcript": "XM_017006645.3",
"protein_id": "XP_016862134.1",
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"cds_start": -4,
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"feature": null
}
],
"gene_symbol": "LZTFL1",
"gene_hgnc_id": 6741,
"dbsnp": "rs12639224",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.253,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001405920.1",
"gene_symbol": "LZTFL1",
"hgnc_id": 6741,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.28-36679G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}