← Back to variant description
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: 11-1753559-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=1753559&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 1753559,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000236671.7",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1183A>T",
"hgvs_p": "p.Thr395Ser",
"transcript": "NM_001909.5",
"protein_id": "NP_001900.1",
"transcript_support_level": null,
"aa_start": 395,
"aa_end": null,
"aa_length": 412,
"cds_start": 1183,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1251,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": "ENST00000236671.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1183A>T",
"hgvs_p": "p.Thr395Ser",
"transcript": "ENST00000236671.7",
"protein_id": "ENSP00000236671.2",
"transcript_support_level": 1,
"aa_start": 395,
"aa_end": null,
"aa_length": 412,
"cds_start": 1183,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1251,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": "NM_001909.5",
"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": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250644",
"gene_hgnc_id": null,
"hgvs_c": "c.1071+244A>T",
"hgvs_p": null,
"transcript": "ENST00000636615.1",
"protein_id": "ENSP00000490014.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 557,
"cds_start": -4,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1300A>T",
"hgvs_p": "p.Thr434Ser",
"transcript": "ENST00000438213.6",
"protein_id": "ENSP00000415036.2",
"transcript_support_level": 2,
"aa_start": 434,
"aa_end": null,
"aa_length": 451,
"cds_start": 1300,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1368,
"cdna_end": null,
"cdna_length": 1544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1177A>T",
"hgvs_p": "p.Thr393Ser",
"transcript": "ENST00000636843.1",
"protein_id": "ENSP00000490897.1",
"transcript_support_level": 5,
"aa_start": 393,
"aa_end": null,
"aa_length": 410,
"cds_start": 1177,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 1512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1174A>T",
"hgvs_p": "p.Thr392Ser",
"transcript": "ENST00000637915.1",
"protein_id": "ENSP00000490471.1",
"transcript_support_level": 5,
"aa_start": 392,
"aa_end": null,
"aa_length": 409,
"cds_start": 1174,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 1211,
"cdna_end": null,
"cdna_length": 1982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1165A>T",
"hgvs_p": "p.Thr389Ser",
"transcript": "ENST00000637815.2",
"protein_id": "ENSP00000490344.1",
"transcript_support_level": 5,
"aa_start": 389,
"aa_end": null,
"aa_length": 406,
"cds_start": 1165,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 1212,
"cdna_end": null,
"cdna_length": 2019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1162A>T",
"hgvs_p": "p.Thr388Ser",
"transcript": "ENST00000636571.1",
"protein_id": "ENSP00000490770.1",
"transcript_support_level": 5,
"aa_start": 388,
"aa_end": null,
"aa_length": 405,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 1230,
"cdna_end": null,
"cdna_length": 1790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1162A>T",
"hgvs_p": "p.Thr388Ser",
"transcript": "ENST00000637387.1",
"protein_id": "ENSP00000490598.1",
"transcript_support_level": 5,
"aa_start": 388,
"aa_end": null,
"aa_length": 405,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 1244,
"cdna_end": null,
"cdna_length": 1597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1078A>T",
"hgvs_p": "p.Thr360Ser",
"transcript": "ENST00000367196.4",
"protein_id": "ENSP00000356164.4",
"transcript_support_level": 5,
"aa_start": 360,
"aa_end": null,
"aa_length": 377,
"cds_start": 1078,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 1386,
"cdna_end": null,
"cdna_length": 2190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "c.1078A>T",
"hgvs_p": "p.Thr360Ser",
"transcript": "ENST00000429746.2",
"protein_id": "ENSP00000402586.2",
"transcript_support_level": 3,
"aa_start": 360,
"aa_end": null,
"aa_length": 377,
"cds_start": 1078,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 1169,
"cdna_end": null,
"cdna_length": 1973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250644",
"gene_hgnc_id": null,
"hgvs_c": "c.607A>T",
"hgvs_p": "p.Thr203Ser",
"transcript": "ENST00000427721.3",
"protein_id": "ENSP00000415840.3",
"transcript_support_level": 2,
"aa_start": 203,
"aa_end": null,
"aa_length": 334,
"cds_start": 607,
"cds_end": null,
"cds_length": 1006,
"cdna_start": 608,
"cdna_end": null,
"cdna_length": 1007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.*349A>T",
"hgvs_p": null,
"transcript": "ENST00000433655.6",
"protein_id": "ENSP00000404902.1",
"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": 2035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.781A>T",
"hgvs_p": null,
"transcript": "ENST00000637158.1",
"protein_id": null,
"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": 1200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.3611A>T",
"hgvs_p": null,
"transcript": "ENST00000637381.2",
"protein_id": null,
"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": 4408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.491A>T",
"hgvs_p": null,
"transcript": "ENST00000637937.1",
"protein_id": null,
"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": 1262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.*1044A>T",
"hgvs_p": null,
"transcript": "ENST00000678991.1",
"protein_id": "ENSP00000503019.1",
"transcript_support_level": null,
"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": 2198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.*349A>T",
"hgvs_p": null,
"transcript": "ENST00000433655.6",
"protein_id": "ENSP00000404902.1",
"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": 2035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.*1044A>T",
"hgvs_p": null,
"transcript": "ENST00000678991.1",
"protein_id": "ENSP00000503019.1",
"transcript_support_level": null,
"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": 2198,
"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": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250644",
"gene_hgnc_id": null,
"hgvs_c": "c.1071+244A>T",
"hgvs_p": null,
"transcript": "ENST00000636397.1",
"protein_id": "ENSP00000489910.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 582,
"cds_start": -4,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4038,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250644",
"gene_hgnc_id": null,
"hgvs_c": "c.72+244A>T",
"hgvs_p": null,
"transcript": "ENST00000636579.1",
"protein_id": "ENSP00000490489.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 73,
"cds_start": -4,
"cds_end": null,
"cds_length": 222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 350,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"hgvs_c": "n.*93A>T",
"hgvs_p": null,
"transcript": "ENST00000497544.3",
"protein_id": null,
"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": 798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CTSD",
"gene_hgnc_id": 2529,
"dbsnp": "rs778724059",
"frequency_reference_population": 6.845564e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84556e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5355886816978455,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.227,
"revel_prediction": "Benign",
"alphamissense_score": 0.199,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.246,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000236671.7",
"gene_symbol": "CTSD",
"hgnc_id": 2529,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1183A>T",
"hgvs_p": "p.Thr395Ser"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000636615.1",
"gene_symbol": "ENSG00000250644",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1071+244A>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
}