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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: 6-46588126-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=46588126&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 46588126,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_016593.5",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.1069T>C",
"hgvs_p": "p.Tyr357His",
"transcript": "NM_016593.5",
"protein_id": "NP_057677.2",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 469,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1305,
"cdna_end": null,
"cdna_length": 2432,
"mane_select": "ENST00000275016.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.1069T>C",
"hgvs_p": "p.Tyr357His",
"transcript": "ENST00000275016.3",
"protein_id": "ENSP00000275016.2",
"transcript_support_level": 1,
"aa_start": 357,
"aa_end": null,
"aa_length": 469,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1305,
"cdna_end": null,
"cdna_length": 2432,
"mane_select": "NM_016593.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.553T>C",
"hgvs_p": "p.Tyr185His",
"transcript": "ENST00000619708.4",
"protein_id": "ENSP00000477769.1",
"transcript_support_level": 1,
"aa_start": 185,
"aa_end": null,
"aa_length": 297,
"cds_start": 553,
"cds_end": null,
"cds_length": 894,
"cdna_start": 1142,
"cdna_end": null,
"cdna_length": 2269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.1009T>C",
"hgvs_p": "p.Tyr337His",
"transcript": "NM_001278738.2",
"protein_id": "NP_001265667.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 449,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 2372,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.553T>C",
"hgvs_p": "p.Tyr185His",
"transcript": "NM_001278739.2",
"protein_id": "NP_001265668.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 297,
"cds_start": 553,
"cds_end": null,
"cds_length": 894,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 2257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.1069T>C",
"hgvs_p": "p.Tyr357His",
"transcript": "XM_017010921.2",
"protein_id": "XP_016866410.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 471,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1416,
"cdna_start": 1305,
"cdna_end": null,
"cdna_length": 2098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.1009T>C",
"hgvs_p": "p.Tyr337His",
"transcript": "XM_017010922.2",
"protein_id": "XP_016866411.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 451,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 2038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.961T>C",
"hgvs_p": "p.Tyr321His",
"transcript": "XM_017010923.2",
"protein_id": "XP_016866412.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 435,
"cds_start": 961,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 1197,
"cdna_end": null,
"cdna_length": 1990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.961T>C",
"hgvs_p": "p.Tyr321His",
"transcript": "XM_017010924.2",
"protein_id": "XP_016866413.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 433,
"cds_start": 961,
"cds_end": null,
"cds_length": 1302,
"cdna_start": 1197,
"cdna_end": null,
"cdna_length": 2324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.1069T>C",
"hgvs_p": "p.Tyr357His",
"transcript": "XM_005249171.5",
"protein_id": "XP_005249228.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 420,
"cds_start": 1069,
"cds_end": null,
"cds_length": 1263,
"cdna_start": 1305,
"cdna_end": null,
"cdna_length": 3870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.1009T>C",
"hgvs_p": "p.Tyr337His",
"transcript": "XM_047418858.1",
"protein_id": "XP_047274814.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 400,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 3810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.961T>C",
"hgvs_p": "p.Tyr321His",
"transcript": "XM_047418859.1",
"protein_id": "XP_047274815.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 384,
"cds_start": 961,
"cds_end": null,
"cds_length": 1155,
"cdna_start": 1197,
"cdna_end": null,
"cdna_length": 3762,
"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": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "n.380T>C",
"hgvs_p": null,
"transcript": "ENST00000480804.1",
"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": 403,
"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": "RCAN2-DT",
"gene_hgnc_id": 55661,
"hgvs_c": "n.403-17805A>G",
"hgvs_p": null,
"transcript": "ENST00000657801.2",
"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": 755,
"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": "RCAN2-DT",
"gene_hgnc_id": 55661,
"hgvs_c": "n.379-17805A>G",
"hgvs_p": null,
"transcript": "ENST00000762069.1",
"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": 729,
"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": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"hgvs_c": "c.1065+7861T>C",
"hgvs_p": null,
"transcript": "XM_047418860.1",
"protein_id": "XP_047274816.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": -4,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CYP39A1",
"gene_hgnc_id": 17449,
"dbsnp": "rs771986688",
"frequency_reference_population": 0.000041246953,
"hom_count_reference_population": 0,
"allele_count_reference_population": 65,
"gnomad_exomes_af": 0.0000435466,
"gnomad_genomes_af": 0.0000197223,
"gnomad_exomes_ac": 62,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3791540265083313,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.196,
"revel_prediction": "Benign",
"alphamissense_score": 0.1678,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.543,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016593.5",
"gene_symbol": "CYP39A1",
"hgnc_id": 17449,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1069T>C",
"hgvs_p": "p.Tyr357His"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000657801.2",
"gene_symbol": "RCAN2-DT",
"hgnc_id": 55661,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.403-17805A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}