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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: X-131288648-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=131288648&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 131288648,
"ref": "G",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000361420.8",
"consequences": [
{
"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": 20,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "NM_001555.5",
"protein_id": "NP_001546.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1336,
"cds_start": -4,
"cds_end": null,
"cds_length": 4011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4461,
"mane_select": "ENST00000361420.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 20,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "ENST00000361420.8",
"protein_id": "ENSP00000355010.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1336,
"cds_start": -4,
"cds_end": null,
"cds_length": 4011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4461,
"mane_select": "NM_001555.5",
"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": 20,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "ENST00000370903.8",
"protein_id": "ENSP00000359940.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1341,
"cds_start": -4,
"cds_end": null,
"cds_length": 4026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4476,
"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": 19,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "ENST00000370910.5",
"protein_id": "ENSP00000359947.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1327,
"cds_start": -4,
"cds_end": null,
"cds_length": 3984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4406,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "ENST00000370901.4",
"protein_id": "ENSP00000359938.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 242,
"cds_start": -4,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1820,
"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": 20,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "NM_001170961.2",
"protein_id": "NP_001164432.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1341,
"cds_start": -4,
"cds_end": null,
"cds_length": 4026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4476,
"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": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "NM_001438811.1",
"protein_id": "NP_001425740.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1341,
"cds_start": -4,
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"cds_length": 4026,
"cdna_start": null,
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"cdna_length": 4497,
"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": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "NM_001438812.1",
"protein_id": "NP_001425741.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1336,
"cds_start": -4,
"cds_end": null,
"cds_length": 4011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4482,
"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": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "NM_001438813.1",
"protein_id": "NP_001425742.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1336,
"cds_start": -4,
"cds_end": null,
"cds_length": 4011,
"cdna_start": null,
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"cdna_length": 4478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "ENST00000651556.1",
"protein_id": "ENSP00000498789.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 19,
"intron_rank": 1,
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"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "NM_001170962.2",
"protein_id": "NP_001164433.1",
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},
{
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"consequences": [
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],
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"gene_symbol": "IGSF1",
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"transcript": "ENST00000370904.6",
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},
{
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],
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"gene_symbol": "IGSF1",
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"hgvs_c": "c.-68+566C>A",
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"transcript": "NM_001438814.1",
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},
{
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],
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"gene_symbol": "IGSF1",
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"hgvs_c": "c.-68+566C>A",
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"transcript": "NM_001438815.1",
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},
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],
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},
{
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"strand": false,
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],
"exon_rank": null,
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"gene_symbol": "IGSF1",
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},
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"hgvs_c": "c.-68+566C>A",
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"transcript": "NM_205833.4",
"protein_id": "NP_991402.1",
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},
{
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],
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"gene_symbol": "IGSF1",
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"hgvs_c": "c.-68+374C>A",
"hgvs_p": null,
"transcript": "ENST00000370900.5",
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},
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],
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"exon_count": 3,
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},
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],
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},
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],
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"gene_symbol": "ENSG00000287806",
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},
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],
"exon_rank": null,
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"intron_rank": 2,
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"gene_symbol": "IGSF1",
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"hgvs_c": "c.-68+566C>A",
"hgvs_p": null,
"transcript": "XM_047442085.1",
"protein_id": "XP_047298041.1",
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
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"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 18,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.-68+566C>A",
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"transcript": "XM_011531334.3",
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"transcript_support_level": null,
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}
],
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"dbsnp": "rs4073307",
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"hom_count_reference_population": 8220,
"allele_count_reference_population": 22680,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.205412,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 22680,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 1811,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.329,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000361420.8",
"gene_symbol": "IGSF1",
"hgnc_id": 5948,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.-68+566C>A",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000773800.1",
"gene_symbol": "ENSG00000287806",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.560+69175G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}