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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: 3-31580004-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=31580004&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 31580004,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_178862.3",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "NM_178862.3",
"protein_id": "NP_849193.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 826,
"cds_start": 619,
"cds_end": null,
"cds_length": 2481,
"cdna_start": 693,
"cdna_end": null,
"cdna_length": 4107,
"mane_select": "ENST00000295770.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_178862.3"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000295770.4",
"protein_id": "ENSP00000295770.2",
"transcript_support_level": 1,
"aa_start": 207,
"aa_end": null,
"aa_length": 826,
"cds_start": 619,
"cds_end": null,
"cds_length": 2481,
"cdna_start": 693,
"cdna_end": null,
"cdna_length": 4107,
"mane_select": "NM_178862.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295770.4"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "n.980A>G",
"hgvs_p": null,
"transcript": "ENST00000453168.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1888,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000453168.5"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000935233.1",
"protein_id": "ENSP00000605292.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 824,
"cds_start": 619,
"cds_end": null,
"cds_length": 2475,
"cdna_start": 1022,
"cdna_end": null,
"cdna_length": 4436,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935233.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000868023.1",
"protein_id": "ENSP00000538082.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 804,
"cds_start": 619,
"cds_end": null,
"cds_length": 2415,
"cdna_start": 991,
"cdna_end": null,
"cdna_length": 4346,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868023.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000935235.1",
"protein_id": "ENSP00000605294.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 793,
"cds_start": 619,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 994,
"cdna_end": null,
"cdna_length": 2931,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935235.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000935232.1",
"protein_id": "ENSP00000605291.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 788,
"cds_start": 619,
"cds_end": null,
"cds_length": 2367,
"cdna_start": 1032,
"cdna_end": null,
"cdna_length": 4330,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935232.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000945188.1",
"protein_id": "ENSP00000615247.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 777,
"cds_start": 619,
"cds_end": null,
"cds_length": 2334,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 3768,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945188.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000945187.1",
"protein_id": "ENSP00000615246.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 774,
"cds_start": 619,
"cds_end": null,
"cds_length": 2325,
"cdna_start": 623,
"cdna_end": null,
"cdna_length": 3880,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945187.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000935234.1",
"protein_id": "ENSP00000605293.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 773,
"cds_start": 619,
"cds_end": null,
"cds_length": 2322,
"cdna_start": 992,
"cdna_end": null,
"cdna_length": 4247,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935234.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000945185.1",
"protein_id": "ENSP00000615244.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 758,
"cds_start": 619,
"cds_end": null,
"cds_length": 2277,
"cdna_start": 1075,
"cdna_end": null,
"cdna_length": 4285,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945185.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000868024.1",
"protein_id": "ENSP00000538083.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 755,
"cds_start": 619,
"cds_end": null,
"cds_length": 2268,
"cdna_start": 915,
"cdna_end": null,
"cdna_length": 4122,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868024.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000868025.1",
"protein_id": "ENSP00000538084.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 754,
"cds_start": 619,
"cds_end": null,
"cds_length": 2265,
"cdna_start": 757,
"cdna_end": null,
"cdna_length": 3954,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868025.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000945186.1",
"protein_id": "ENSP00000615245.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 745,
"cds_start": 619,
"cds_end": null,
"cds_length": 2238,
"cdna_start": 1023,
"cdna_end": null,
"cdna_length": 4196,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945186.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "ENST00000945184.1",
"protein_id": "ENSP00000615243.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 733,
"cds_start": 619,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1097,
"cdna_end": null,
"cdna_length": 4230,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945184.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.181A>G",
"hgvs_p": "p.Ile61Val",
"transcript": "ENST00000462235.6",
"protein_id": "ENSP00000520729.1",
"transcript_support_level": 3,
"aa_start": 61,
"aa_end": null,
"aa_length": 680,
"cds_start": 181,
"cds_end": null,
"cds_length": 2043,
"cdna_start": 432,
"cdna_end": null,
"cdna_length": 3305,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000462235.6"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.181A>G",
"hgvs_p": "p.Ile61Val",
"transcript": "ENST00000463044.2",
"protein_id": "ENSP00000520728.1",
"transcript_support_level": 3,
"aa_start": 61,
"aa_end": null,
"aa_length": 658,
"cds_start": 181,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 513,
"cdna_end": null,
"cdna_length": 3056,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000463044.2"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.181A>G",
"hgvs_p": "p.Ile61Val",
"transcript": "XM_017005858.2",
"protein_id": "XP_016861347.1",
"transcript_support_level": null,
"aa_start": 61,
"aa_end": null,
"aa_length": 680,
"cds_start": 181,
"cds_end": null,
"cds_length": 2043,
"cdna_start": 428,
"cdna_end": null,
"cdna_length": 3842,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005858.2"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val",
"transcript": "XM_011533465.2",
"protein_id": "XP_011531767.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 444,
"cds_start": 619,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 693,
"cdna_end": null,
"cdna_length": 3320,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533465.2"
},
{
"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": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "c.423+3500A>G",
"hgvs_p": null,
"transcript": "ENST00000718294.1",
"protein_id": "ENSP00000520727.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 730,
"cds_start": null,
"cds_end": null,
"cds_length": 2193,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4751,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000718294.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"hgvs_c": "n.646A>G",
"hgvs_p": null,
"transcript": "ENST00000423527.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1664,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000423527.5"
}
],
"gene_symbol": "STT3B",
"gene_hgnc_id": 30611,
"dbsnp": "rs780102016",
"frequency_reference_population": 0.000021689635,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000225769,
"gnomad_genomes_af": 0.0000131577,
"gnomad_exomes_ac": 33,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.49961307644844055,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.11999999731779099,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.451,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0876,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.325,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.12,
"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": "NM_178862.3",
"gene_symbol": "STT3B",
"hgnc_id": 30611,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.619A>G",
"hgvs_p": "p.Ile207Val"
}
],
"clinvar_disease": "STT3B-congenital disorder of glycosylation",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "STT3B-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}