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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: 2-239280101-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=239280101&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 239280101,
"ref": "T",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000543185.6",
"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": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.23-43437A>T",
"hgvs_p": null,
"transcript": "NM_001378414.1",
"protein_id": "NP_001365343.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1089,
"cds_start": -4,
"cds_end": null,
"cds_length": 3270,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8461,
"mane_select": "ENST00000543185.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.23-43437A>T",
"hgvs_p": null,
"transcript": "ENST00000543185.6",
"protein_id": "ENSP00000440481.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1089,
"cds_start": -4,
"cds_end": null,
"cds_length": 3270,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8461,
"mane_select": "NM_001378414.1",
"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": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.23-43437A>T",
"hgvs_p": null,
"transcript": "ENST00000345617.7",
"protein_id": "ENSP00000264606.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1084,
"cds_start": -4,
"cds_end": null,
"cds_length": 3255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8976,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "n.474+18065A>T",
"hgvs_p": null,
"transcript": "ENST00000463007.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "n.495-43437A>T",
"hgvs_p": null,
"transcript": "ENST00000493582.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3188,
"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": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.23-43437A>T",
"hgvs_p": null,
"transcript": "NM_001378415.1",
"protein_id": "NP_001365344.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1089,
"cds_start": -4,
"cds_end": null,
"cds_length": 3270,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8666,
"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": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.23-43437A>T",
"hgvs_p": null,
"transcript": "NM_001378416.1",
"protein_id": "NP_001365345.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1084,
"cds_start": -4,
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"cds_length": 3255,
"cdna_start": null,
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"cdna_length": 8446,
"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": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.23-43437A>T",
"hgvs_p": null,
"transcript": "NM_001378417.1",
"protein_id": "NP_001365346.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1084,
"cds_start": -4,
"cds_end": null,
"cds_length": 3255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8651,
"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": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.23-43437A>T",
"hgvs_p": null,
"transcript": "NM_006037.4",
"protein_id": "NP_006028.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1084,
"cds_start": -4,
"cds_end": null,
"cds_length": 3255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9047,
"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": 16,
"intron_rank": 1,
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"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.7+18065A>T",
"hgvs_p": null,
"transcript": "NM_001435996.1",
"protein_id": "NP_001422925.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 763,
"cds_start": -4,
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"cds_length": 2292,
"cdna_start": null,
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"cdna_length": 3702,
"mane_select": null,
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"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": 4,
"intron_rank": 1,
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"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.-60+28986A>T",
"hgvs_p": null,
"transcript": "ENST00000446876.1",
"protein_id": "ENSP00000392912.1",
"transcript_support_level": 4,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
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],
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"exon_count": 16,
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"gene_symbol": "HDAC4",
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"hgvs_c": "n.365+18065A>T",
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"transcript": "ENST00000535493.5",
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},
{
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],
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"gene_symbol": "HDAC4",
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"hgvs_c": "n.298-28901A>T",
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},
{
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"strand": false,
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],
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},
{
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],
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},
{
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],
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"gene_symbol": "HDAC4",
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"hgvs_c": "n.285-43437A>T",
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},
{
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],
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"transcript": "XM_011512217.3",
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},
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],
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"gene_symbol": "HDAC4",
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"hgvs_c": "c.94+28439A>T",
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"transcript": "XM_006712877.4",
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},
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],
"exon_rank": null,
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"gene_symbol": "HDAC4",
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"hgvs_c": "c.94+28439A>T",
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],
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],
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},
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],
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"gene_symbol": "HDAC4",
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"hgvs_c": "c.23-43437A>T",
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"transcript": "XM_011512222.4",
"protein_id": "XP_011510524.1",
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"feature": null
},
{
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"strand": false,
"consequences": [
"intron_variant"
],
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"intron_rank": 2,
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"gene_symbol": "HDAC4",
"gene_hgnc_id": 14063,
"hgvs_c": "c.23-43437A>T",
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},
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},
{
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{
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}
],
"gene_symbol": "HDAC4",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0,
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"gnomad_genomes_ac": 0,
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"computational_score_selected": -1.0099999904632568,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"bayesdelnoaf_score": -1.01,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.604,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_score": -4,
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"acmg_by_gene": [
{
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"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000543185.6",
"gene_symbol": "HDAC4",
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"effects": [
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],
"inheritance_mode": "AD,Unknown",
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}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}