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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: 3-15455986-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=15455986&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COLQ",
"hgnc_id": 2226,
"hgvs_c": "c.1108G>T",
"hgvs_p": "p.Asp370Tyr",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_005677.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000293553",
"hgnc_id": null,
"hgvs_c": "n.-46G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 3,
"score": 3,
"transcript": "ENST00000629729.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,PP3",
"acmg_score": 4,
"allele_count_reference_population": 15,
"alphamissense_prediction": null,
"alphamissense_score": 0.0985,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.05,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7603085041046143,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 455,
"aa_ref": "D",
"aa_start": 370,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2960,
"cdna_start": 1189,
"cds_end": null,
"cds_length": 1368,
"cds_start": 1108,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_005677.4",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1108G>T",
"hgvs_p": "p.Asp370Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000383788.10",
"protein_coding": true,
"protein_id": "NP_005668.2",
"strand": false,
"transcript": "NM_005677.4",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 455,
"aa_ref": "D",
"aa_start": 370,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2960,
"cdna_start": 1189,
"cds_end": null,
"cds_length": 1368,
"cds_start": 1108,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000383788.10",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1108G>T",
"hgvs_p": "p.Asp370Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005677.4",
"protein_coding": true,
"protein_id": "ENSP00000373298.3",
"strand": false,
"transcript": "ENST00000383788.10",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 456,
"aa_ref": "D",
"aa_start": 370,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1668,
"cdna_start": 1234,
"cds_end": null,
"cds_length": 1371,
"cds_start": 1108,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000603808.5",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1108G>T",
"hgvs_p": "p.Asp370Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000474271.1",
"strand": false,
"transcript": "ENST00000603808.5",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 460,
"aa_ref": "D",
"aa_start": 375,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3066,
"cdna_start": 1295,
"cds_end": null,
"cds_length": 1383,
"cds_start": 1123,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000874202.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1123G>T",
"hgvs_p": "p.Asp375Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544261.1",
"strand": false,
"transcript": "ENST00000874202.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 455,
"aa_ref": "D",
"aa_start": 370,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2924,
"cdna_start": 1185,
"cds_end": null,
"cds_length": 1368,
"cds_start": 1108,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000959102.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1108G>T",
"hgvs_p": "p.Asp370Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629161.1",
"strand": false,
"transcript": "ENST00000959102.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 448,
"aa_ref": "D",
"aa_start": 363,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2937,
"cdna_start": 1169,
"cds_end": null,
"cds_length": 1347,
"cds_start": 1087,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000959107.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1087G>T",
"hgvs_p": "p.Asp363Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629166.1",
"strand": false,
"transcript": "ENST00000959107.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 446,
"aa_ref": "D",
"aa_start": 361,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2989,
"cdna_start": 1217,
"cds_end": null,
"cds_length": 1341,
"cds_start": 1081,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000874203.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1081G>T",
"hgvs_p": "p.Asp361Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544262.1",
"strand": false,
"transcript": "ENST00000874203.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 445,
"aa_ref": "D",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3134,
"cdna_start": 1363,
"cds_end": null,
"cds_length": 1338,
"cds_start": 1078,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_080538.2",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1078G>T",
"hgvs_p": "p.Asp360Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_536799.1",
"strand": false,
"transcript": "NM_080538.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 445,
"aa_ref": "D",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2784,
"cdna_start": 1363,
"cds_end": null,
"cds_length": 1338,
"cds_start": 1078,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000383781.8",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1078G>T",
"hgvs_p": "p.Asp360Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000373291.3",
"strand": false,
"transcript": "ENST00000383781.8",
"transcript_support_level": 5
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 439,
"aa_ref": "D",
"aa_start": 354,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2909,
"cdna_start": 1139,
"cds_end": null,
"cds_length": 1320,
"cds_start": 1060,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000874205.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1060G>T",
"hgvs_p": "p.Asp354Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544264.1",
"strand": false,
"transcript": "ENST00000874205.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 422,
"aa_ref": "D",
"aa_start": 337,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2870,
"cdna_start": 1104,
"cds_end": null,
"cds_length": 1269,
"cds_start": 1009,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000874204.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1009G>T",
"hgvs_p": "p.Asp337Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544263.1",
"strand": false,
"transcript": "ENST00000874204.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 421,
"aa_ref": "D",
"aa_start": 336,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2858,
"cdna_start": 1087,
"cds_end": null,
"cds_length": 1266,
"cds_start": 1006,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_080539.4",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1006G>T",
"hgvs_p": "p.Asp336Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_536800.2",
"strand": false,
"transcript": "NM_080539.4",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 421,
"aa_ref": "D",
"aa_start": 336,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1482,
"cdna_start": 1117,
"cds_end": null,
"cds_length": 1266,
"cds_start": 1006,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000383786.9",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.1006G>T",
"hgvs_p": "p.Asp336Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000373296.3",
"strand": false,
"transcript": "ENST00000383786.9",
"transcript_support_level": 5
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 401,
"aa_ref": "D",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2806,
"cdna_start": 1037,
"cds_end": null,
"cds_length": 1206,
"cds_start": 946,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000959106.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.946G>T",
"hgvs_p": "p.Asp316Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629165.1",
"strand": false,
"transcript": "ENST00000959106.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 388,
"aa_ref": "D",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2788,
"cdna_start": 1027,
"cds_end": null,
"cds_length": 1167,
"cds_start": 907,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000959105.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.907G>T",
"hgvs_p": "p.Asp303Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629164.1",
"strand": false,
"transcript": "ENST00000959105.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 378,
"aa_ref": "D",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2813,
"cdna_start": 1074,
"cds_end": null,
"cds_length": 1137,
"cds_start": 907,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000959103.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.907G>T",
"hgvs_p": "p.Asp303Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629162.1",
"strand": false,
"transcript": "ENST00000959103.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 328,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2612,
"cdna_start": null,
"cds_end": null,
"cds_length": 987,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000959104.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.815-2055G>T",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629163.1",
"strand": false,
"transcript": "ENST00000959104.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1771,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000604401.2",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "n.964G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000604401.2",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2947,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000679838.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "n.*870G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505708.1",
"strand": false,
"transcript": "ENST00000679838.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1682,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000680240.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "n.1020G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000680240.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2605,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
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}