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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: 14-92143004-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=92143004&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "CPSF2",
"hgnc_id": 2325,
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_017437.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 4,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.4144,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "14",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.2356274425983429,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13003,
"cdna_start": 1103,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_017437.3",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000298875.9",
"protein_coding": true,
"protein_id": "NP_059133.1",
"strand": true,
"transcript": "NM_017437.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 13003,
"cdna_start": 1103,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000298875.9",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017437.3",
"protein_coding": true,
"protein_id": "ENSP00000298875.4",
"strand": true,
"transcript": "ENST00000298875.9",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13226,
"cdna_start": 1326,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001322272.2",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001309201.1",
"strand": true,
"transcript": "NM_001322272.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6678,
"cdna_start": 1191,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000908829.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578888.1",
"strand": true,
"transcript": "ENST00000908829.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5317,
"cdna_start": 1362,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000932645.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602704.1",
"strand": true,
"transcript": "ENST00000932645.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4378,
"cdna_start": 1232,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000932646.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602705.1",
"strand": true,
"transcript": "ENST00000932646.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4143,
"cdna_start": 1247,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000932647.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602706.1",
"strand": true,
"transcript": "ENST00000932647.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2906,
"cdna_start": 1086,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000932649.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602708.1",
"strand": true,
"transcript": "ENST00000932649.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6402,
"cdna_start": 2452,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000932650.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602709.1",
"strand": true,
"transcript": "ENST00000932650.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 782,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5131,
"cdna_start": 1182,
"cds_end": null,
"cds_length": 2349,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000943809.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000613868.1",
"strand": true,
"transcript": "ENST00000943809.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 767,
"aa_ref": "V",
"aa_start": 269,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2989,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 2304,
"cds_start": 805,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000908831.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.805G>A",
"hgvs_p": "p.Val269Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578890.1",
"strand": true,
"transcript": "ENST00000908831.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 731,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12850,
"cdna_start": 1103,
"cds_end": null,
"cds_length": 2196,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001322270.2",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001309199.1",
"strand": true,
"transcript": "NM_001322270.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 682,
"aa_ref": "V",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3368,
"cdna_start": 1106,
"cds_end": null,
"cds_length": 2049,
"cds_start": 850,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000908830.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.850G>A",
"hgvs_p": "p.Val284Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578889.1",
"strand": true,
"transcript": "ENST00000908830.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 629,
"aa_ref": "V",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12843,
"cdna_start": 943,
"cds_end": null,
"cds_length": 1890,
"cds_start": 391,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001322271.2",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.391G>A",
"hgvs_p": "p.Val131Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001309200.1",
"strand": true,
"transcript": "NM_001322271.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 685,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2616,
"cdna_start": null,
"cds_end": null,
"cds_length": 2058,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000932648.1",
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"hgvs_c": "c.849+653G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602707.1",
"strand": true,
"transcript": "ENST00000932648.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.542377585624351,
"dbsnp": "rs375811121",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": 0.0000027539902,
"gene_hgnc_id": 2325,
"gene_symbol": "CPSF2",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000275399,
"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": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.802,
"pos": 92143004,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.264,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.4959999918937683,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.2,
"transcript": "NM_017437.3"
}
]
}