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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: 12-110645045-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=110645045&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 110645045,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000397659.9",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1410C>T",
"hgvs_p": "p.Tyr470Tyr",
"transcript": "NM_001082538.3",
"protein_id": "NP_001076007.1",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 592,
"cds_start": 1410,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1464,
"cdna_end": null,
"cdna_length": 2222,
"mane_select": "ENST00000397659.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1410C>T",
"hgvs_p": "p.Tyr470Tyr",
"transcript": "ENST00000397659.9",
"protein_id": "ENSP00000380779.4",
"transcript_support_level": 1,
"aa_start": 470,
"aa_end": null,
"aa_length": 592,
"cds_start": 1410,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1464,
"cdna_end": null,
"cdna_length": 2222,
"mane_select": "NM_001082538.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1410C>T",
"hgvs_p": "p.Tyr470Tyr",
"transcript": "ENST00000551590.5",
"protein_id": "ENSP00000448735.1",
"transcript_support_level": 1,
"aa_start": 470,
"aa_end": null,
"aa_length": 587,
"cds_start": 1410,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 1566,
"cdna_end": null,
"cdna_length": 2309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1368C>T",
"hgvs_p": "p.Tyr456Tyr",
"transcript": "ENST00000397655.7",
"protein_id": "ENSP00000380775.3",
"transcript_support_level": 1,
"aa_start": 456,
"aa_end": null,
"aa_length": 573,
"cds_start": 1368,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1438,
"cdna_end": null,
"cdna_length": 1879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "n.*1043C>T",
"hgvs_p": null,
"transcript": "ENST00000397656.8",
"protein_id": "ENSP00000380776.4",
"transcript_support_level": 2,
"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": 2098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "n.*1236C>T",
"hgvs_p": null,
"transcript": "ENST00000464809.5",
"protein_id": "ENSP00000435027.1",
"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": 1996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "n.*686C>T",
"hgvs_p": null,
"transcript": "ENST00000480648.5",
"protein_id": "ENSP00000437196.1",
"transcript_support_level": 5,
"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": 1891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "n.*1168C>T",
"hgvs_p": null,
"transcript": "ENST00000495659.6",
"protein_id": "ENSP00000436673.2",
"transcript_support_level": 2,
"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": 1988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "n.*1043C>T",
"hgvs_p": null,
"transcript": "ENST00000397656.8",
"protein_id": "ENSP00000380776.4",
"transcript_support_level": 2,
"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": 2098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "n.*1236C>T",
"hgvs_p": null,
"transcript": "ENST00000464809.5",
"protein_id": "ENSP00000435027.1",
"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": 1996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "n.*686C>T",
"hgvs_p": null,
"transcript": "ENST00000480648.5",
"protein_id": "ENSP00000437196.1",
"transcript_support_level": 5,
"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": 1891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "n.*1168C>T",
"hgvs_p": null,
"transcript": "ENST00000495659.6",
"protein_id": "ENSP00000436673.2",
"transcript_support_level": 2,
"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": 1988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1183C>T",
"hgvs_p": "p.Arg395Cys",
"transcript": "ENST00000471804.7",
"protein_id": "ENSP00000473903.2",
"transcript_support_level": 3,
"aa_start": 395,
"aa_end": null,
"aa_length": 397,
"cds_start": 1183,
"cds_end": null,
"cds_length": 1195,
"cdna_start": 1253,
"cdna_end": null,
"cdna_length": 1265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1183C>T",
"hgvs_p": "p.Arg395Cys",
"transcript": "XM_011538737.4",
"protein_id": "XP_011537039.1",
"transcript_support_level": null,
"aa_start": 395,
"aa_end": null,
"aa_length": 516,
"cds_start": 1183,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 1237,
"cdna_end": null,
"cdna_length": 1994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1141C>T",
"hgvs_p": "p.Arg381Cys",
"transcript": "XM_047429538.1",
"protein_id": "XP_047285494.1",
"transcript_support_level": null,
"aa_start": 381,
"aa_end": null,
"aa_length": 502,
"cds_start": 1141,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 1195,
"cdna_end": null,
"cdna_length": 1952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1057C>T",
"hgvs_p": "p.Arg353Cys",
"transcript": "XM_011538738.4",
"protein_id": "XP_011537040.1",
"transcript_support_level": null,
"aa_start": 353,
"aa_end": null,
"aa_length": 474,
"cds_start": 1057,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 1868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1015C>T",
"hgvs_p": "p.Arg339Cys",
"transcript": "XM_047429539.1",
"protein_id": "XP_047285495.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 460,
"cds_start": 1015,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 1298,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1183C>T",
"hgvs_p": "p.Arg395Cys",
"transcript": "XM_047429540.1",
"protein_id": "XP_047285496.1",
"transcript_support_level": null,
"aa_start": 395,
"aa_end": null,
"aa_length": 443,
"cds_start": 1183,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1237,
"cdna_end": null,
"cdna_length": 1462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1183C>T",
"hgvs_p": "p.Arg395Cys",
"transcript": "XM_047429541.1",
"protein_id": "XP_047285497.1",
"transcript_support_level": null,
"aa_start": 395,
"aa_end": null,
"aa_length": 438,
"cds_start": 1183,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 1237,
"cdna_end": null,
"cdna_length": 1447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1057C>T",
"hgvs_p": "p.Arg353Cys",
"transcript": "XM_047429543.1",
"protein_id": "XP_047285499.1",
"transcript_support_level": null,
"aa_start": 353,
"aa_end": null,
"aa_length": 396,
"cds_start": 1057,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 1321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.649C>T",
"hgvs_p": "p.Arg217Cys",
"transcript": "XM_047429544.1",
"protein_id": "XP_047285500.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 338,
"cds_start": 649,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 1116,
"cdna_end": null,
"cdna_length": 1873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1410C>T",
"hgvs_p": "p.Tyr470Tyr",
"transcript": "NM_001082537.3",
"protein_id": "NP_001076006.1",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 587,
"cds_start": 1410,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 1464,
"cdna_end": null,
"cdna_length": 2207,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TCTN1",
"gene_hgnc_id": 26113,
"hgvs_c": "c.1368C>T",
"hgvs_p": "p.Tyr456Tyr",
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"frequency_reference_population": 0.00019700185,
"hom_count_reference_population": 1,
"allele_count_reference_population": 318,
"gnomad_exomes_af": 0.000113552,
"gnomad_genomes_af": 0.000997912,
"gnomad_exomes_ac": 166,
"gnomad_genomes_ac": 152,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4169999957084656,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.417,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3094,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.468,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6,BP7,BS1",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP6",
"BP7",
"BS1"
],
"verdict": "Likely_benign",
"transcript": "ENST00000397659.9",
"gene_symbol": "TCTN1",
"hgnc_id": 26113,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1410C>T",
"hgvs_p": "p.Tyr470Tyr"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000548312.5",
"gene_symbol": "HVCN1",
"hgnc_id": 28240,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.756+5123G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Joubert syndrome,Meckel-Gruber syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3",
"phenotype_combined": "not specified|not provided|Joubert syndrome;Meckel-Gruber syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}