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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: 1-11801333-A-AGGGTCACCTGCTGGGTGCCAGGTCACGTCTATGTAGAGG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=11801333&ref=A&alt=AGGGTCACCTGCTGGGTGCCAGGTCACGTCTATGTAGAGG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 11801333,
"ref": "A",
"alt": "AGGGTCACCTGCTGGGTGCCAGGTCACGTCTATGTAGAGG",
"effect": "disruptive_inframe_insertion",
"transcript": "ENST00000376590.9",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "PLYIDVTWHPAGDP",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "NM_005957.5",
"protein_id": "NP_005948.3",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 656,
"cds_start": 302,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 392,
"cdna_end": null,
"cdna_length": 7018,
"mane_select": "ENST00000376590.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PLYIDVTWHPAGDP",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "ENST00000376590.9",
"protein_id": "ENSP00000365775.3",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 656,
"cds_start": 302,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 392,
"cdna_end": null,
"cdna_length": 7018,
"mane_select": "NM_005957.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PLYIDVTWHPAGDP",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.384_422dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro141_Gly142insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "ENST00000423400.7",
"protein_id": "ENSP00000398908.3",
"transcript_support_level": 1,
"aa_start": 141,
"aa_end": null,
"aa_length": 696,
"cds_start": 422,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 2715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PLYIDVTWHPAGDP",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "ENST00000376592.6",
"protein_id": "ENSP00000365777.1",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 656,
"cds_start": 302,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1752,
"cdna_end": null,
"cdna_length": 8378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PLYIDVTWHPAGDP",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "ENST00000376486.3",
"protein_id": "ENSP00000365669.3",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 228,
"cds_start": 302,
"cds_end": null,
"cds_length": 689,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 875,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "n.1062_1100dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": null,
"transcript": "ENST00000431243.6",
"protein_id": null,
"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": 1116,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PLYIDVTWHPAGDP",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.387_425dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro142_Gly143insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "NM_001330358.2",
"protein_id": "NP_001317287.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 697,
"cds_start": 425,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 448,
"cdna_end": null,
"cdna_length": 7074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PLYIDVTWHPAGDP",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.387_425dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro142_Gly143insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "ENST00000376583.7",
"protein_id": "ENSP00000365767.3",
"transcript_support_level": 5,
"aa_start": 142,
"aa_end": null,
"aa_length": 697,
"cds_start": 425,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 425,
"cdna_end": null,
"cdna_length": 7044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.387_425dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro142_Gly143insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "ENST00000376585.6",
"protein_id": "ENSP00000365770.1",
"transcript_support_level": 5,
"aa_start": 142,
"aa_end": null,
"aa_length": 697,
"cds_start": 425,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 1477,
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"cdna_length": 8094,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
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"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.384_422dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro141_Gly142insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "NM_001410750.1",
"protein_id": "NP_001397679.1",
"transcript_support_level": null,
"aa_start": 141,
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"aa_length": 696,
"cds_start": 422,
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"cdna_start": 445,
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"mane_select": null,
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"feature": null
},
{
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"strand": false,
"consequences": [
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],
"exon_rank": 2,
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"exon_count": 11,
"intron_rank": null,
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"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "ENST00000641407.1",
"protein_id": "ENSP00000493098.1",
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"cds_start": 302,
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"cdna_start": 569,
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"mane_select": null,
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": 3,
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"intron_rank": null,
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"gene_symbol": "MTHFR",
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"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "ENST00000418034.1",
"protein_id": "ENSP00000405082.1",
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},
{
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],
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"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
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"hgvs_p": "p.Pro142_Gly143insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "XM_011541496.4",
"protein_id": "XP_011539798.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": 3,
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"intron_rank": null,
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"gene_symbol": "MTHFR",
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"hgvs_c": "c.384_422dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro141_Gly142insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "XM_047421174.1",
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},
{
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],
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"gene_symbol": "MTHFR",
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"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "XM_005263462.5",
"protein_id": "XP_005263519.1",
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},
{
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],
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"intron_rank": null,
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"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "XM_047421178.1",
"protein_id": "XP_047277134.1",
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},
{
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],
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"gene_symbol": "MTHFR",
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"hgvs_c": "c.387_425dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro142_Gly143insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "XM_017001328.3",
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},
{
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],
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"gene_symbol": "MTHFR",
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"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "XM_047421179.1",
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},
{
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"consequences": [
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],
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"intron_rank": null,
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"gene_symbol": "MTHFR",
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"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "XM_047421180.1",
"protein_id": "XP_047277136.1",
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},
{
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"consequences": [
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],
"exon_rank": 3,
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"gene_symbol": "MTHFR",
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"hgvs_c": "c.264_302dupCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCC",
"hgvs_p": "p.Pro101_Gly102insLeuTyrIleAspValThrTrpHisProAlaGlyAspPro",
"transcript": "XM_047421181.1",
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}
],
"gene_symbol": "MTHFR",
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"hom_count_reference_population": 0,
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"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.202,
"phylop100way_prediction": "Pathogenic",
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"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
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"acmg_by_gene": [
{
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"benign_score": 0,
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"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
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],
"clinvar_disease": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}