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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: 8-140695007-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=140695007&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 140695007,
"ref": "C",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000696786.1",
"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": 36,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2622+5884G>T",
"hgvs_p": null,
"transcript": "NM_001352702.2",
"protein_id": "NP_001339631.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1096,
"cds_start": -4,
"cds_end": null,
"cds_length": 3291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5136,
"mane_select": "ENST00000696786.1",
"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": 36,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2622+5884G>T",
"hgvs_p": null,
"transcript": "ENST00000696786.1",
"protein_id": "ENSP00000512868.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1096,
"cds_start": -4,
"cds_end": null,
"cds_length": 3291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5136,
"mane_select": "NM_001352702.2",
"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": 32,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2499+5884G>T",
"hgvs_p": null,
"transcript": "ENST00000521059.5",
"protein_id": "ENSP00000429474.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1052,
"cds_start": -4,
"cds_end": null,
"cds_length": 3159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4405,
"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": 32,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2499+5884G>T",
"hgvs_p": null,
"transcript": "ENST00000522684.5",
"protein_id": "ENSP00000429911.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1052,
"cds_start": -4,
"cds_end": null,
"cds_length": 3159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4955,
"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": 29,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2391+5884G>T",
"hgvs_p": null,
"transcript": "ENST00000519654.5",
"protein_id": "ENSP00000429929.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1016,
"cds_start": -4,
"cds_end": null,
"cds_length": 3051,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4129,
"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": 18,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.1383+5884G>T",
"hgvs_p": null,
"transcript": "ENST00000519465.5",
"protein_id": "ENSP00000429170.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 680,
"cds_start": -4,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3279,
"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": 33,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "n.*2170+5884G>T",
"hgvs_p": null,
"transcript": "ENST00000519993.5",
"protein_id": "ENSP00000428570.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 4388,
"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": 26,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "n.*1063+5884G>T",
"hgvs_p": null,
"transcript": "ENST00000524202.5",
"protein_id": "ENSP00000429023.1",
"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": 3014,
"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": 36,
"intron_rank": 31,
"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2754+5884G>T",
"hgvs_p": null,
"transcript": "NM_001352697.2",
"protein_id": "NP_001339626.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1116,
"cds_start": -4,
"cds_end": null,
"cds_length": 3351,
"cdna_start": null,
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"cdna_length": 5461,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 36,
"intron_rank": 29,
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"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2670+5884G>T",
"hgvs_p": null,
"transcript": "NM_001387649.1",
"protein_id": "NP_001374578.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1112,
"cds_start": -4,
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"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": 36,
"intron_rank": 29,
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"gene_symbol": "PTK2",
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"hgvs_c": "c.2661+5884G>T",
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"transcript": "NM_001352698.2",
"protein_id": "NP_001339627.1",
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},
{
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"consequences": [
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],
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"gene_symbol": "PTK2",
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},
{
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"strand": false,
"consequences": [
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],
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"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2631+5884G>T",
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"transcript": "NM_001387662.1",
"protein_id": "NP_001374591.1",
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},
{
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"consequences": [
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],
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"gene_symbol": "PTK2",
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"hgvs_c": "c.2622+5884G>T",
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"transcript": "NM_001352699.2",
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},
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],
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"gene_symbol": "PTK2",
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"hgvs_c": "c.2622+5884G>T",
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"transcript": "NM_001352700.2",
"protein_id": "NP_001339629.1",
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},
{
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],
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"gene_symbol": "PTK2",
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"transcript": "NM_001352701.2",
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},
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],
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"gene_symbol": "PTK2",
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"hgvs_c": "c.2622+5884G>T",
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"transcript": "NM_001352703.2",
"protein_id": "NP_001339632.1",
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},
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],
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"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2631+5884G>T",
"hgvs_p": null,
"transcript": "NM_001387643.1",
"protein_id": "NP_001374572.1",
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},
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],
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"gene_symbol": "PTK2",
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"hgvs_c": "c.2631+5884G>T",
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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": "PTK2",
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"hgvs_c": "c.2631+5884G>T",
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"transcript": "NM_001387660.1",
"protein_id": "NP_001374589.1",
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},
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"protein_coding": true,
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"consequences": [
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],
"exon_rank": null,
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"exon_count": 34,
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"intron_rank_end": null,
"gene_symbol": "PTK2",
"gene_hgnc_id": 9611,
"hgvs_c": "c.2631+5884G>T",
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"protein_id": "XP_047278010.1",
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}
],
"gene_symbol": "PTK2",
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"dbsnp": "rs7839119",
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"hom_count_reference_population": 3681,
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"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.219694,
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"gnomad_genomes_ac": 33415,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 3681,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -1,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.788,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000696786.1",
"gene_symbol": "PTK2",
"hgnc_id": 9611,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2622+5884G>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
}