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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: 1-33864232-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=33864232&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 33864232,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_145205.6",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGB4",
"gene_hgnc_id": 24954,
"hgvs_c": "c.41C>G",
"hgvs_p": "p.Ser14Cys",
"transcript": "NM_001379301.1",
"protein_id": "NP_001366230.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 186,
"cds_start": 41,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000681531.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379301.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGB4",
"gene_hgnc_id": 24954,
"hgvs_c": "c.41C>G",
"hgvs_p": "p.Ser14Cys",
"transcript": "ENST00000681531.1",
"protein_id": "ENSP00000505691.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 186,
"cds_start": 41,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001379301.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000681531.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGB4",
"gene_hgnc_id": 24954,
"hgvs_c": "c.41C>G",
"hgvs_p": "p.Ser14Cys",
"transcript": "ENST00000519684.5",
"protein_id": "ENSP00000429214.1",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 186,
"cds_start": 41,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000519684.5"
},
{
"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": 71,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.921-17236G>C",
"hgvs_p": null,
"transcript": "NM_001281956.2",
"protein_id": "NP_001268885.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3631,
"cds_start": null,
"cds_end": null,
"cds_length": 10896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000373381.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001281956.2"
},
{
"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": 71,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.921-17236G>C",
"hgvs_p": null,
"transcript": "ENST00000373381.9",
"protein_id": "ENSP00000362479.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 3631,
"cds_start": null,
"cds_end": null,
"cds_length": 10896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001281956.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373381.9"
},
{
"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": 70,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.801-17236G>C",
"hgvs_p": null,
"transcript": "ENST00000373388.7",
"protein_id": "ENSP00000362486.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 3487,
"cds_start": null,
"cds_end": null,
"cds_length": 10464,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373388.7"
},
{
"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": "HMGB4",
"gene_hgnc_id": 24954,
"hgvs_c": "n.102-31C>G",
"hgvs_p": null,
"transcript": "ENST00000425537.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000425537.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGB4",
"gene_hgnc_id": 24954,
"hgvs_c": "c.41C>G",
"hgvs_p": "p.Ser14Cys",
"transcript": "NM_145205.6",
"protein_id": "NP_660206.2",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 186,
"cds_start": 41,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_145205.6"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGB4",
"gene_hgnc_id": 24954,
"hgvs_c": "c.41C>G",
"hgvs_p": "p.Ser14Cys",
"transcript": "ENST00000522796.1",
"protein_id": "ENSP00000430919.1",
"transcript_support_level": 5,
"aa_start": 14,
"aa_end": null,
"aa_length": 186,
"cds_start": 41,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000522796.1"
},
{
"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": 71,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.801-17236G>C",
"hgvs_p": null,
"transcript": "ENST00000619121.4",
"protein_id": "ENSP00000483463.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 3591,
"cds_start": null,
"cds_end": null,
"cds_length": 10776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000619121.4"
},
{
"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": 70,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.801-17236G>C",
"hgvs_p": null,
"transcript": "NM_052896.5",
"protein_id": "NP_443128.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3487,
"cds_start": null,
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"cds_length": 10464,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_052896.5"
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HMGB4",
"gene_hgnc_id": 24954,
"hgvs_c": "c.-151-31C>G",
"hgvs_p": null,
"transcript": "NM_001352984.2",
"protein_id": "NP_001339913.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 112,
"cds_start": null,
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"cds_length": 339,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001352984.2"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.921-17236G>C",
"hgvs_p": null,
"transcript": "XM_017000185.2",
"protein_id": "XP_016855674.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 3607,
"cds_start": null,
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"cds_length": 10824,
"cdna_start": null,
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"mane_select": null,
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"biotype": "protein_coding",
"feature": "XM_017000185.2"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 71,
"intron_rank": 5,
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"gene_symbol": "CSMD2",
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"hgvs_c": "c.921-17236G>C",
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"transcript": "XM_047443607.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.921-17236G>C",
"hgvs_p": null,
"transcript": "XM_047443642.1",
"protein_id": "XP_047299598.1",
"transcript_support_level": null,
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"biotype": "protein_coding",
"feature": "XM_047443642.1"
},
{
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"protein_coding": true,
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],
"exon_rank": null,
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"exon_count": 71,
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"gene_symbol": "CSMD2",
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"hgvs_c": "c.801-17236G>C",
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},
{
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"strand": false,
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],
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"exon_count": 71,
"intron_rank": 5,
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"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.801-17236G>C",
"hgvs_p": null,
"transcript": "XM_047443685.1",
"protein_id": "XP_047299641.1",
"transcript_support_level": null,
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"biotype": "protein_coding",
"feature": "XM_047443685.1"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.921-17236G>C",
"hgvs_p": null,
"transcript": "XM_047443661.1",
"protein_id": "XP_047299617.1",
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"aa_start": null,
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},
{
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"strand": false,
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],
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"intron_rank": 5,
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"gene_symbol": "CSMD2",
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},
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],
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"intron_rank": 5,
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"hgvs_c": "c.921-17236G>C",
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},
{
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"strand": false,
"consequences": [
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],
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"intron_rank": 5,
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"gene_symbol": "CSMD2",
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"hgvs_c": "c.921-17236G>C",
"hgvs_p": null,
"transcript": "XM_017000192.2",
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"biotype": "protein_coding",
"feature": "XM_017000192.2"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CSMD2",
"gene_hgnc_id": 19290,
"hgvs_c": "c.921-17236G>C",
"hgvs_p": null,
"transcript": "XM_017000193.2",
"protein_id": "XP_016855682.1",
"transcript_support_level": null,
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"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
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"biotype": "protein_coding",
"feature": "XM_017000193.2"
}
],
"gene_symbol": "HMGB4",
"gene_hgnc_id": 24954,
"dbsnp": "rs371723682",
"frequency_reference_population": 0.000014266078,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.00000684928,
"gnomad_genomes_af": 0.0000854094,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7478379011154175,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.11999999731779099,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.344,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4983,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.898,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_145205.6",
"gene_symbol": "HMGB4",
"hgnc_id": 24954,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.41C>G",
"hgvs_p": "p.Ser14Cys"
},
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001281956.2",
"gene_symbol": "CSMD2",
"hgnc_id": 19290,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.921-17236G>C",
"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
}