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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: 2-3546023-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=3546023&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "RNASEH1",
"hgnc_id": 18466,
"hgvs_c": "c.775-152G>A",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -10,
"transcript": "NM_002936.6",
"verdict": "Benign"
},
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000286905",
"hgnc_id": null,
"hgvs_c": "n.775-152G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -10,
"transcript": "ENST00000658393.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_score": -10,
"allele_count_reference_population": 890,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.97,
"chr": "2",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.9700000286102295,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 286,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5289,
"cdna_start": null,
"cds_end": null,
"cds_length": 861,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_002936.6",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.775-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000315212.4",
"protein_coding": true,
"protein_id": "NP_002927.2",
"strand": false,
"transcript": "NM_002936.6",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 286,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5289,
"cdna_start": null,
"cds_end": null,
"cds_length": 861,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000315212.4",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.775-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002936.6",
"protein_coding": true,
"protein_id": "ENSP00000313350.3",
"strand": false,
"transcript": "ENST00000315212.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 2742,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000658393.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000286905",
"hgvs_c": "n.775-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499330.1",
"strand": false,
"transcript": "ENST00000658393.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 324,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1748,
"cdna_start": null,
"cds_end": null,
"cds_length": 975,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000861506.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.889-152G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531565.1",
"strand": false,
"transcript": "ENST00000861506.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 286,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5327,
"cdna_start": null,
"cds_end": null,
"cds_length": 861,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000921961.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.775-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592020.1",
"strand": false,
"transcript": "ENST00000921961.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5286,
"cdna_start": null,
"cds_end": null,
"cds_length": 858,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001378272.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.772-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365201.1",
"strand": false,
"transcript": "NM_001378272.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1650,
"cdna_start": null,
"cds_end": null,
"cds_length": 858,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000968504.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.772-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638563.1",
"strand": false,
"transcript": "ENST00000968504.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 281,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5274,
"cdna_start": null,
"cds_end": null,
"cds_length": 846,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001378273.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.760-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365202.1",
"strand": false,
"transcript": "NM_001378273.1",
"transcript_support_level": null
},
{
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"aa_length": 279,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5268,
"cdna_start": null,
"cds_end": null,
"cds_length": 840,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000921962.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.754-152G>A",
"hgvs_p": null,
"intron_rank": 7,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592021.1",
"strand": false,
"transcript": "ENST00000921962.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5309,
"cdna_start": null,
"cds_end": null,
"cds_length": 825,
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"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
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"feature": "NM_001378271.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.775-132G>A",
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365200.1",
"strand": false,
"transcript": "NM_001378271.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5289,
"cdna_start": null,
"cds_end": null,
"cds_length": 783,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
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"feature": "NM_001286834.3",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.697-152G>A",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001273763.1",
"strand": false,
"transcript": "NM_001286834.3",
"transcript_support_level": null
},
{
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"cdna_start": null,
"cds_end": null,
"cds_length": 510,
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"consequences": [
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],
"exon_count": 8,
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"feature": "NM_001286837.3",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "c.424-152G>A",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001273766.1",
"strand": false,
"transcript": "NM_001286837.3",
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},
{
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"biotype": "nonsense_mediated_decay",
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"consequences": [
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],
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"feature": "ENST00000436842.5",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "n.*881-152G>A",
"hgvs_p": null,
"intron_rank": 7,
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000404926.1",
"strand": false,
"transcript": "ENST00000436842.5",
"transcript_support_level": 2
},
{
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"biotype": "nonsense_mediated_decay",
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"cdna_end": null,
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"cds_end": null,
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"consequences": [
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],
"exon_count": 11,
"exon_rank": null,
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"feature": "ENST00000654051.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000286905",
"hgvs_c": "n.775-152G>A",
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"mane_plus": null,
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"protein_id": "ENSP00000499604.1",
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},
{
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"biotype": "pseudogene",
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"consequences": [
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],
"exon_count": 11,
"exon_rank": null,
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"feature": "NR_148532.2",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "n.848-152G>A",
"hgvs_p": null,
"intron_rank": 7,
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"mane_plus": null,
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"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_148532.2",
"transcript_support_level": null
},
{
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"biotype": "pseudogene",
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"consequences": [
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],
"exon_count": 8,
"exon_rank": null,
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"feature": "NR_148533.2",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "n.844-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
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"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_148533.2",
"transcript_support_level": null
},
{
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],
"exon_count": 12,
"exon_rank": null,
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"feature": "NR_148534.2",
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"hgvs_c": "n.848-152G>A",
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},
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],
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"feature": "NR_165465.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "n.732-152G>A",
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"mane_plus": null,
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"protein_id": null,
"strand": false,
"transcript": "NR_165465.1",
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},
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"consequences": [
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],
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"feature": "NR_165466.1",
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"protein_coding": false,
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"strand": false,
"transcript": "NR_165466.1",
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},
{
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"biotype": "pseudogene",
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"cdna_start": null,
"cds_end": null,
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"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_165467.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "n.1017-152G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_165467.1",
"transcript_support_level": null
},
{
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"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_165468.1",
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
"hgvs_c": "n.820-152G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_165468.1",
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}
],
"custom_annotations": null,
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"dbscsnv_ada_score": null,
"dbsnp": "rs115373330",
"effect": "intron_variant",
"frequency_reference_population": 0.001398619,
"gene_hgnc_id": 18466,
"gene_symbol": "RNASEH1",
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"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 11,
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"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.373,
"pos": 3546023,
"ref": "C",
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"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
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"transcript": "NM_002936.6"
}
]
}