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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: 9-113288183-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=113288183&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRPF4",
"hgnc_id": 17349,
"hgvs_c": "c.944C>T",
"hgvs_p": "p.Pro315Leu",
"inheritance_mode": "AD",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_004697.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 12,
"allele_count_reference_population": 4,
"alphamissense_prediction": null,
"alphamissense_score": 0.8498,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.22,
"chr": "9",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "Retinal dystrophy,Retinitis pigmentosa 70,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8603193759918213,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 521,
"aa_ref": "P",
"aa_start": 314,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2897,
"cdna_start": 1027,
"cds_end": null,
"cds_length": 1566,
"cds_start": 941,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001244926.2",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.941C>T",
"hgvs_p": "p.Pro314Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374198.5",
"protein_coding": true,
"protein_id": "NP_001231855.1",
"strand": true,
"transcript": "NM_001244926.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 521,
"aa_ref": "P",
"aa_start": 314,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2897,
"cdna_start": 1027,
"cds_end": null,
"cds_length": 1566,
"cds_start": 941,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000374198.5",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.941C>T",
"hgvs_p": "p.Pro314Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001244926.2",
"protein_coding": true,
"protein_id": "ENSP00000363313.4",
"strand": true,
"transcript": "ENST00000374198.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 522,
"aa_ref": "P",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4020,
"cdna_start": 1046,
"cds_end": null,
"cds_length": 1569,
"cds_start": 944,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000374199.9",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.944C>T",
"hgvs_p": "p.Pro315Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363315.4",
"strand": true,
"transcript": "ENST00000374199.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 609,
"aa_ref": "P",
"aa_start": 314,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2997,
"cdna_start": 996,
"cds_end": null,
"cds_length": 1830,
"cds_start": 941,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000921177.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.941C>T",
"hgvs_p": "p.Pro314Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591236.1",
"strand": true,
"transcript": "ENST00000921177.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 540,
"aa_ref": "P",
"aa_start": 333,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3939,
"cdna_start": 1084,
"cds_end": null,
"cds_length": 1623,
"cds_start": 998,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000921173.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.998C>T",
"hgvs_p": "p.Pro333Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591232.1",
"strand": true,
"transcript": "ENST00000921173.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 522,
"aa_ref": "P",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2900,
"cdna_start": 1030,
"cds_end": null,
"cds_length": 1569,
"cds_start": 944,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_004697.5",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.944C>T",
"hgvs_p": "p.Pro315Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_004688.2",
"strand": true,
"transcript": "NM_004697.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 520,
"aa_ref": "P",
"aa_start": 313,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3989,
"cdna_start": 1024,
"cds_end": null,
"cds_length": 1563,
"cds_start": 938,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000921172.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Pro313Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591231.1",
"strand": true,
"transcript": "ENST00000921172.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 513,
"aa_ref": "P",
"aa_start": 306,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2195,
"cdna_start": 1003,
"cds_end": null,
"cds_length": 1542,
"cds_start": 917,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000894605.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.917C>T",
"hgvs_p": "p.Pro306Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564664.1",
"strand": true,
"transcript": "ENST00000894605.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 506,
"aa_ref": "P",
"aa_start": 314,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2718,
"cdna_start": 1014,
"cds_end": null,
"cds_length": 1521,
"cds_start": 941,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000921176.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.941C>T",
"hgvs_p": "p.Pro314Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591235.1",
"strand": true,
"transcript": "ENST00000921176.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 486,
"aa_ref": "P",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2646,
"cdna_start": 1017,
"cds_end": null,
"cds_length": 1461,
"cds_start": 944,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000894604.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.944C>T",
"hgvs_p": "p.Pro315Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564663.1",
"strand": true,
"transcript": "ENST00000894604.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 485,
"aa_ref": "P",
"aa_start": 314,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2680,
"cdna_start": 1017,
"cds_end": null,
"cds_length": 1458,
"cds_start": 941,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000921174.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.941C>T",
"hgvs_p": "p.Pro314Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591233.1",
"strand": true,
"transcript": "ENST00000921174.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 481,
"aa_ref": "P",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3731,
"cdna_start": 998,
"cds_end": null,
"cds_length": 1446,
"cds_start": 944,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000945708.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.944C>T",
"hgvs_p": "p.Pro315Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615767.1",
"strand": true,
"transcript": "ENST00000945708.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 460,
"aa_ref": "P",
"aa_start": 253,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2583,
"cdna_start": 844,
"cds_end": null,
"cds_length": 1383,
"cds_start": 758,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000921175.1",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.758C>T",
"hgvs_p": "p.Pro253Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591234.1",
"strand": true,
"transcript": "ENST00000921175.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 279,
"aa_ref": "P",
"aa_start": 72,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2936,
"cdna_start": 1066,
"cds_end": null,
"cds_length": 840,
"cds_start": 215,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001322266.2",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.215C>T",
"hgvs_p": "p.Pro72Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001309195.1",
"strand": true,
"transcript": "NM_001322266.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 279,
"aa_ref": "P",
"aa_start": 72,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2939,
"cdna_start": 1069,
"cds_end": null,
"cds_length": 840,
"cds_start": 215,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001322267.2",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "c.215C>T",
"hgvs_p": "p.Pro72Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001309196.1",
"strand": true,
"transcript": "NM_001322267.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2851,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NR_136265.2",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "n.1030C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_136265.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2848,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NR_136266.2",
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"hgvs_c": "n.1027C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_136266.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs587777599",
"effect": "missense_variant",
"frequency_reference_population": 0.0000027363562,
"gene_hgnc_id": 17349,
"gene_symbol": "PRPF4",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000273636,
"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": "Likely pathogenic",
"phenotype_combined": "Retinitis pigmentosa 70|not provided|Retinal dystrophy",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.387,
"pos": 113288183,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.789,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_004697.5"
}
]
}