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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: 3-108355178-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=108355178&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 108355178,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001282556.2",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "NM_001282556.2",
"protein_id": "NP_001269485.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 414,
"cds_start": 482,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 2417,
"mane_select": "ENST00000467761.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "ENST00000467761.6",
"protein_id": "ENSP00000419207.1",
"transcript_support_level": 5,
"aa_start": 161,
"aa_end": null,
"aa_length": 414,
"cds_start": 482,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 2417,
"mane_select": "NM_001282556.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "ENST00000357759.9",
"protein_id": "ENSP00000350402.5",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 414,
"cds_start": 482,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 896,
"cdna_end": null,
"cdna_length": 2666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "ENST00000489514.6",
"protein_id": "ENSP00000417856.2",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 414,
"cds_start": 482,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 636,
"cdna_end": null,
"cdna_length": 2406,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "ENST00000491820.5",
"protein_id": "ENSP00000418284.1",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 397,
"cds_start": 482,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 727,
"cdna_end": null,
"cdna_length": 1439,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "NM_001282557.2",
"protein_id": "NP_001269486.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 414,
"cds_start": 482,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 636,
"cdna_end": null,
"cdna_length": 2406,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "NM_001370244.1",
"protein_id": "NP_001357173.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 414,
"cds_start": 482,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 2408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "NM_007072.4",
"protein_id": "NP_009003.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 414,
"cds_start": 482,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 896,
"cdna_end": null,
"cdna_length": 2666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "NM_001282558.2",
"protein_id": "NP_001269487.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 397,
"cds_start": 482,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 725,
"cdna_end": null,
"cdna_length": 2444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Val97Ala",
"transcript": "NM_001282559.2",
"protein_id": "NP_001269488.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 350,
"cds_start": 290,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 463,
"cdna_end": null,
"cdna_length": 2233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Val97Ala",
"transcript": "ENST00000467562.5",
"protein_id": "ENSP00000418345.1",
"transcript_support_level": 2,
"aa_start": 97,
"aa_end": null,
"aa_length": 350,
"cds_start": 290,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 464,
"cdna_end": null,
"cdna_length": 1457,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
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"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.188T>C",
"hgvs_p": "p.Val63Ala",
"transcript": "ENST00000482099.1",
"protein_id": "ENSP00000418797.1",
"transcript_support_level": 2,
"aa_start": 63,
"aa_end": null,
"aa_length": 327,
"cds_start": 188,
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"cds_length": 984,
"cdna_start": 189,
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"cdna_length": 2659,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
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],
"exon_rank": 6,
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"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "XM_011512362.3",
"protein_id": "XP_011510664.1",
"transcript_support_level": null,
"aa_start": 161,
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"aa_length": 425,
"cds_start": 482,
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"cdna_start": 725,
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},
{
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"protein_coding": true,
"strand": true,
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],
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"exon_count": 9,
"intron_rank": null,
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"gene_symbol": "HHLA2",
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"transcript": "XM_011512363.3",
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},
{
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],
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"intron_rank": null,
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"gene_symbol": "HHLA2",
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"hgvs_c": "c.482T>C",
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"transcript": "XM_011512364.3",
"protein_id": "XP_011510666.1",
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"cdna_start": 647,
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"biotype": null,
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},
{
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"strand": true,
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],
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"gene_symbol": "HHLA2",
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"transcript": "XM_024453326.2",
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},
{
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],
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"gene_symbol": "HHLA2",
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"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "XM_047447368.1",
"protein_id": "XP_047303324.1",
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": true,
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],
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"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "XM_047447369.1",
"protein_id": "XP_047303325.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 425,
"cds_start": 482,
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"cdna_start": 3180,
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"mane_select": null,
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},
{
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"protein_coding": true,
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],
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"exon_count": 11,
"intron_rank": null,
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"gene_symbol": "HHLA2",
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"hgvs_c": "c.482T>C",
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"transcript": "XM_005247080.4",
"protein_id": "XP_005247137.1",
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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": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala",
"transcript": "XM_011512367.4",
"protein_id": "XP_011510669.1",
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"aa_start": 161,
"aa_end": null,
"aa_length": 379,
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"cdna_start": 725,
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"biotype": null,
"feature": null
},
{
"aa_ref": "V",
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
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"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.383T>C",
"hgvs_p": "p.Val128Ala",
"transcript": "ENST00000467282.5",
"protein_id": "ENSP00000420622.1",
"transcript_support_level": 3,
"aa_start": 128,
"aa_end": null,
"aa_length": 127,
"cds_start": 383,
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"cdna_start": 567,
"cdna_end": null,
"cdna_length": 568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"hgvs_c": "c.*48T>C",
"hgvs_p": null,
"transcript": "ENST00000463019.7",
"protein_id": "ENSP00000419940.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 143,
"cds_start": -4,
"cds_end": null,
"cds_length": 434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HHLA2",
"gene_hgnc_id": 4905,
"dbsnp": "rs757473905",
"frequency_reference_population": 0.000011774826,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.000012317,
"gnomad_genomes_af": 0.0000065697,
"gnomad_exomes_ac": 18,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2576831579208374,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.112,
"revel_prediction": "Benign",
"alphamissense_score": 0.1803,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.627,
"phylop100way_prediction": "Benign",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001282556.2",
"gene_symbol": "HHLA2",
"hgnc_id": 4905,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Val161Ala"
}
],
"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
}