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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: 3-157442272-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=157442272&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 157442272,
"ref": "A",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000362010.7",
"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": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.530-13784T>A",
"hgvs_p": null,
"transcript": "NM_001167912.2",
"protein_id": "NP_001161384.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 833,
"cds_start": -4,
"cds_end": null,
"cds_length": 2502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4191,
"mane_select": "ENST00000362010.7",
"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": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.530-13784T>A",
"hgvs_p": null,
"transcript": "ENST00000362010.7",
"protein_id": "ENSP00000354919.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 833,
"cds_start": -4,
"cds_end": null,
"cds_length": 2502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4191,
"mane_select": "NM_001167912.2",
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTX3",
"gene_hgnc_id": 9692,
"hgvs_c": "c.533-94A>T",
"hgvs_p": null,
"transcript": "NM_002852.4",
"protein_id": "NP_002843.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 381,
"cds_start": -4,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1884,
"mane_select": "ENST00000295927.4",
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTX3",
"gene_hgnc_id": 9692,
"hgvs_c": "c.533-94A>T",
"hgvs_p": null,
"transcript": "ENST00000295927.4",
"protein_id": "ENSP00000295927.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 381,
"cds_start": -4,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1884,
"mane_select": "NM_002852.4",
"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": 4,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.530-13784T>A",
"hgvs_p": null,
"transcript": "ENST00000392833.6",
"protein_id": "ENSP00000376578.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 788,
"cds_start": -4,
"cds_end": null,
"cds_length": 2367,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3979,
"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": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.530-13784T>A",
"hgvs_p": null,
"transcript": "NM_024621.2",
"protein_id": "NP_078897.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 833,
"cds_start": -4,
"cds_end": null,
"cds_length": 2502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4313,
"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": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.530-13784T>A",
"hgvs_p": null,
"transcript": "ENST00000392832.6",
"protein_id": "ENSP00000376577.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 833,
"cds_start": -4,
"cds_end": null,
"cds_length": 2502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3044,
"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": 4,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.530-13784T>A",
"hgvs_p": null,
"transcript": "NM_001167911.2",
"protein_id": "NP_001161383.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 788,
"cds_start": -4,
"cds_end": null,
"cds_length": 2367,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4056,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.194-13784T>A",
"hgvs_p": null,
"transcript": "ENST00000479987.5",
"protein_id": "ENSP00000418963.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 119,
"cds_start": -4,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 665,
"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": 13,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.563-13784T>A",
"hgvs_p": null,
"transcript": "XM_011513134.3",
"protein_id": "XP_011511436.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 844,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 3996,
"mane_select": null,
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"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": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "VEPH1",
"gene_hgnc_id": 25735,
"hgvs_c": "c.530-13784T>A",
"hgvs_p": null,
"transcript": "XM_024453746.2",
"protein_id": "XP_024309514.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"transcript": "XM_024453747.2",
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},
{
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"consequences": [
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],
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"gene_symbol": "VEPH1",
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"hgvs_c": "c.530-13784T>A",
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"transcript": "XM_024453748.2",
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},
{
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"strand": false,
"consequences": [
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],
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"gene_symbol": "VEPH1",
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},
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],
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"transcript": "XM_047448921.1",
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},
{
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],
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"gene_symbol": "VEPH1",
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"hgvs_c": "c.530-13784T>A",
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"transcript": "XM_047448922.1",
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],
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},
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],
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"gene_symbol": "VEPH1",
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"hgvs_c": "c.194-13784T>A",
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"transcript": "XM_047448924.1",
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],
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"gene_symbol": "VEPH1",
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"hgvs_c": "c.530-13784T>A",
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"transcript": "XM_047448928.1",
"protein_id": "XP_047304884.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 4,
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"gene_symbol": "VEPH1",
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"hgvs_c": "c.530-13784T>A",
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"transcript": "XM_047448929.1",
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},
{
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}
],
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"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
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"splice_prediction_selected": "Benign",
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"bayesdelnoaf_score": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.045,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_score": -2,
"acmg_classification": "Likely_benign",
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"acmg_by_gene": [
{
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000362010.7",
"gene_symbol": "VEPH1",
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"effects": [
"intron_variant"
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"inheritance_mode": "AR",
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},
{
"score": -2,
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"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000295927.4",
"gene_symbol": "PTX3",
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"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
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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
}