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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: 13-52024566-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=52024566&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 52024566,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000521508.2",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "c.836A>C",
"hgvs_p": "p.Tyr279Ser",
"transcript": "NM_001004127.3",
"protein_id": "NP_001004127.2",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 492,
"cds_start": 836,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 6510,
"mane_select": "ENST00000521508.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "c.836A>C",
"hgvs_p": "p.Tyr279Ser",
"transcript": "ENST00000521508.2",
"protein_id": "ENSP00000430236.1",
"transcript_support_level": 1,
"aa_start": 279,
"aa_end": null,
"aa_length": 492,
"cds_start": 836,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 6510,
"mane_select": "NM_001004127.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "c.836A>C",
"hgvs_p": "p.Tyr279Ser",
"transcript": "ENST00000649340.2",
"protein_id": "ENSP00000497184.2",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 491,
"cds_start": 836,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 5097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "c.605A>C",
"hgvs_p": "p.Tyr202Ser",
"transcript": "ENST00000681053.1",
"protein_id": "ENSP00000505307.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 415,
"cds_start": 605,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 6219,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.3772A>C",
"hgvs_p": null,
"transcript": "ENST00000519151.1",
"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": 4574,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.5140A>C",
"hgvs_p": null,
"transcript": "ENST00000649651.2",
"protein_id": null,
"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": 10733,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.*588A>C",
"hgvs_p": null,
"transcript": "ENST00000679359.1",
"protein_id": "ENSP00000505579.1",
"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": 6504,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.739A>C",
"hgvs_p": null,
"transcript": "ENST00000680058.1",
"protein_id": null,
"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": 6332,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.963A>C",
"hgvs_p": null,
"transcript": "ENST00000680950.1",
"protein_id": null,
"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": 6556,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.*561A>C",
"hgvs_p": null,
"transcript": "ENST00000681047.1",
"protein_id": "ENSP00000505034.1",
"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": 6454,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.*588A>C",
"hgvs_p": null,
"transcript": "ENST00000679359.1",
"protein_id": "ENSP00000505579.1",
"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": 6504,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.*561A>C",
"hgvs_p": null,
"transcript": "ENST00000681047.1",
"protein_id": "ENSP00000505034.1",
"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": 6454,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "c.275+5423A>C",
"hgvs_p": null,
"transcript": "ENST00000649708.2",
"protein_id": "ENSP00000497459.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 117,
"cds_start": -4,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 997,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "c.276-3753A>C",
"hgvs_p": null,
"transcript": "ENST00000679544.1",
"protein_id": "ENSP00000505560.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 113,
"cds_start": -4,
"cds_end": null,
"cds_length": 342,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5510,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "c.*1-3756A>C",
"hgvs_p": null,
"transcript": "ENST00000681145.1",
"protein_id": "ENSP00000505163.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 92,
"cds_start": -4,
"cds_end": null,
"cds_length": 279,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1520,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "c.45-3753A>C",
"hgvs_p": null,
"transcript": "ENST00000523764.1",
"protein_id": "ENSP00000429497.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 36,
"cds_start": -4,
"cds_end": null,
"cds_length": 111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1404,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.276-20A>C",
"hgvs_p": null,
"transcript": "ENST00000650049.2",
"protein_id": "ENSP00000497398.2",
"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": 1004,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.44+12104A>C",
"hgvs_p": null,
"transcript": "ENST00000679495.1",
"protein_id": null,
"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": 669,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.2200-3753A>C",
"hgvs_p": null,
"transcript": "ENST00000680793.1",
"protein_id": null,
"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": 6052,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.396-3753A>C",
"hgvs_p": null,
"transcript": "ENST00000681226.1",
"protein_id": null,
"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": 4248,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"hgvs_c": "n.66-3753A>C",
"hgvs_p": null,
"transcript": "NR_036571.3",
"protein_id": null,
"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": 5347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UTP14C",
"gene_hgnc_id": 20321,
"hgvs_c": "c.-858A>C",
"hgvs_p": null,
"transcript": "NM_021645.6",
"protein_id": "NP_067677.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 766,
"cds_start": -4,
"cds_end": null,
"cds_length": 2301,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5529,
"mane_select": "ENST00000521776.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UTP14C",
"gene_hgnc_id": 20321,
"hgvs_c": "c.-858A>C",
"hgvs_p": null,
"transcript": "ENST00000521776.2",
"protein_id": "ENSP00000428619.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 766,
"cds_start": -4,
"cds_end": null,
"cds_length": 2301,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5529,
"mane_select": "NM_021645.6",
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALG11",
"gene_hgnc_id": 32456,
"dbsnp": "rs387907181",
"frequency_reference_population": 0.0000027362253,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273623,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9115074276924133,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.917,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7981,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.886,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.13,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000521508.2",
"gene_symbol": "ALG11",
"hgnc_id": 32456,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.836A>C",
"hgvs_p": "p.Tyr279Ser"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000521776.2",
"gene_symbol": "UTP14C",
"hgnc_id": 20321,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-858A>C",
"hgvs_p": null
}
],
"clinvar_disease": "ALG11-congenital disorder of glycosylation,ALG11-related disorder",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "ALG11-congenital disorder of glycosylation|ALG11-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}