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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: 2-58108546-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=58108546&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 58108546,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000340157.9",
"consequences": [
{
"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": 13,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.544-14555T>C",
"hgvs_p": null,
"transcript": "NM_006296.7",
"protein_id": "NP_006287.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 508,
"cds_start": -4,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1773,
"mane_select": "ENST00000340157.9",
"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": 13,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.544-14555T>C",
"hgvs_p": null,
"transcript": "ENST00000340157.9",
"protein_id": "ENSP00000342381.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 508,
"cds_start": -4,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1773,
"mane_select": "NM_006296.7",
"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": 16,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.544-14555T>C",
"hgvs_p": null,
"transcript": "ENST00000435505.6",
"protein_id": "ENSP00000408002.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 508,
"cds_start": -4,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2446,
"mane_select": null,
"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": 13,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.475-14555T>C",
"hgvs_p": null,
"transcript": "ENST00000440705.6",
"protein_id": "ENSP00000398323.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 485,
"cds_start": -4,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1676,
"mane_select": null,
"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": 12,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.190-14555T>C",
"hgvs_p": null,
"transcript": "ENST00000412104.6",
"protein_id": "ENSP00000404156.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 390,
"cds_start": -4,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "n.*501-14555T>C",
"hgvs_p": null,
"transcript": "ENST00000432057.2",
"protein_id": "ENSP00000400006.1",
"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": 1870,
"mane_select": null,
"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": 13,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.544-14555T>C",
"hgvs_p": null,
"transcript": "NM_001130480.2",
"protein_id": "NP_001123952.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 508,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1939,
"mane_select": null,
"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": 13,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.544-14555T>C",
"hgvs_p": null,
"transcript": "NM_001130481.2",
"protein_id": "NP_001123953.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 508,
"cds_start": -4,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1781,
"mane_select": null,
"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": 16,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "VRK2",
"gene_hgnc_id": 12719,
"hgvs_c": "c.544-14555T>C",
"hgvs_p": null,
"transcript": "NM_001288837.2",
"protein_id": "NP_001275766.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 508,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2509,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 13,
"intron_rank": 7,
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"gene_symbol": "VRK2",
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"hgvs_c": "c.475-14555T>C",
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"transcript": "NM_001130482.2",
"protein_id": "NP_001123954.1",
"transcript_support_level": null,
"aa_start": null,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 19,
"intron_rank": 12,
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"gene_symbol": "VRK2",
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"hgvs_c": "c.544-14555T>C",
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"transcript": "ENST00000648897.1",
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},
{
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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": "VRK2",
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],
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},
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],
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],
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"gene_symbol": "ENSG00000303851",
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},
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],
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"hgvs_c": "c.544-14555T>C",
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"transcript": "XM_005264540.5",
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"intron_rank": 7,
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],
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"gene_symbol": "VRK2",
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"hgvs_c": "c.190-14555T>C",
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"transcript": "XM_047445745.1",
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},
{
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],
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"exon_count": 10,
"intron_rank": 4,
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"gene_symbol": "VRK2",
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},
{
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],
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"gnomad_genomes_ac": 47789,
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"computational_score_selected": -0.8700000047683716,
"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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"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.87,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.238,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
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"acmg_score": -12,
"acmg_classification": "Benign",
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"acmg_by_gene": [
{
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"benign_score": 12,
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"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000340157.9",
"gene_symbol": "VRK2",
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"effects": [
"intron_variant"
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"inheritance_mode": "AR",
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{
"score": -12,
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"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000797496.1",
"gene_symbol": "ENSG00000303851",
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"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.253-7029A>G",
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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
}