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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: 6-35214477-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=35214477&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SCUBE3",
"hgnc_id": 13655,
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_152753.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000305352",
"hgnc_id": null,
"hgvs_c": "n.262-21867G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000810546.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1068,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "6",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.16126751899719238,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 993,
"aa_ref": "A",
"aa_start": 20,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7819,
"cdna_start": 522,
"cds_end": null,
"cds_length": 2982,
"cds_start": 59,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_152753.4",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000274938.8",
"protein_coding": true,
"protein_id": "NP_689966.2",
"strand": true,
"transcript": "NM_152753.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 993,
"aa_ref": "A",
"aa_start": 20,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7819,
"cdna_start": 522,
"cds_end": null,
"cds_length": 2982,
"cds_start": 59,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000274938.8",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_152753.4",
"protein_coding": true,
"protein_id": "ENSP00000274938.7",
"strand": true,
"transcript": "ENST00000274938.8",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 1009,
"aa_ref": "A",
"aa_start": 20,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4477,
"cdna_start": 520,
"cds_end": null,
"cds_length": 3030,
"cds_start": 59,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000889524.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559583.1",
"strand": true,
"transcript": "ENST00000889524.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 1008,
"aa_ref": "A",
"aa_start": 20,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3523,
"cdna_start": 446,
"cds_end": null,
"cds_length": 3027,
"cds_start": 59,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000940915.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610974.1",
"strand": true,
"transcript": "ENST00000940915.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 992,
"aa_ref": "A",
"aa_start": 20,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7816,
"cdna_start": 522,
"cds_end": null,
"cds_length": 2979,
"cds_start": 59,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001303136.2",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001290065.1",
"strand": true,
"transcript": "NM_001303136.2",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 992,
"aa_ref": "A",
"aa_start": 20,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7914,
"cdna_start": 619,
"cds_end": null,
"cds_length": 2979,
"cds_start": 59,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000926754.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596813.1",
"strand": true,
"transcript": "ENST00000926754.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 979,
"aa_ref": "A",
"aa_start": 20,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4216,
"cdna_start": 522,
"cds_end": null,
"cds_length": 2940,
"cds_start": 59,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000889525.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559584.1",
"strand": true,
"transcript": "ENST00000889525.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
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"aa_length": 955,
"aa_ref": "A",
"aa_start": 20,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3935,
"cdna_start": 313,
"cds_end": null,
"cds_length": 2868,
"cds_start": 59,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000889526.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559585.1",
"strand": true,
"transcript": "ENST00000889526.1",
"transcript_support_level": null
},
{
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"aa_length": 954,
"aa_ref": "A",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3026,
"cdna_start": 82,
"cds_end": null,
"cds_length": 2865,
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"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000940916.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610975.1",
"strand": true,
"transcript": "ENST00000940916.1",
"transcript_support_level": null
},
{
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"aa_ref": "A",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3262,
"cdna_start": 329,
"cds_end": null,
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"consequences": [
"missense_variant"
],
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"feature": "ENST00000889527.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000559586.1",
"strand": true,
"transcript": "ENST00000889527.1",
"transcript_support_level": null
},
{
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"aa_ref": "A",
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"canonical": false,
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"cdna_start": 175,
"cds_end": null,
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"consequences": [
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],
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"feature": "ENST00000889528.1",
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"mane_plus": null,
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"protein_coding": true,
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"strand": true,
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},
{
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],
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"feature": "ENST00000926755.1",
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"strand": true,
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},
{
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"consequences": [
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],
"exon_count": 20,
"exon_rank": 1,
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"feature": "ENST00000940913.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
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"mane_plus": null,
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"protein_coding": true,
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"strand": true,
"transcript": "ENST00000940913.1",
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},
{
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],
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"feature": "ENST00000940914.1",
"gene_hgnc_id": 13655,
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"protein_id": "ENSP00000610973.1",
"strand": true,
"transcript": "ENST00000940914.1",
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},
{
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"cds_end": null,
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"consequences": [
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],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_005248943.2",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005249000.1",
"strand": true,
"transcript": "XM_005248943.2",
"transcript_support_level": null
},
{
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"aa_ref": "A",
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 7705,
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"cds_end": null,
"cds_length": 2868,
"cds_start": 59,
"consequences": [
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],
"exon_count": 22,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_005248947.2",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.59C>T",
"hgvs_p": "p.Ala20Val",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_005249004.1",
"strand": true,
"transcript": "XM_005248947.2",
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},
{
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"aa_ref": "A",
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"consequences": [
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],
"exon_count": 21,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_047418383.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
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"protein_coding": true,
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"strand": true,
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},
{
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"biotype": "pseudogene",
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"cdna_end": null,
"cdna_length": 903,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000810546.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000305352",
"hgvs_c": "n.262-21867G>A",
"hgvs_p": null,
"intron_rank": 2,
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000810546.1",
"transcript_support_level": null
},
{
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"biotype": "pseudogene",
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"cdna_end": null,
"cdna_length": 1098,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000810547.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000305352",
"hgvs_c": "n.457-21867G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000810547.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 985,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10790,
"cdna_start": null,
"cds_end": null,
"cds_length": 2958,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047418382.1",
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"hgvs_c": "c.-3661C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047274338.1",
"strand": true,
"transcript": "XM_047418382.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1782807002",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 13655,
"gene_symbol": "SCUBE3",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.562,
"pos": 35214477,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.156,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_152753.4"
}
]
}