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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: 17-1673487-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=1673487&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate",
"BP6_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRPF8",
"hgnc_id": 17340,
"hgvs_c": "c.3527C>T",
"hgvs_p": "p.Ser1176Phe",
"inheritance_mode": "AD",
"pathogenic_score": 5,
"score": 3,
"transcript": "NM_006445.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,PP3_Moderate,BP6_Moderate",
"acmg_score": 3,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9977,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.42,
"chr": "17",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Irido-corneo-trabecular dysgenesis",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9148058295249939,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2335,
"aa_ref": "S",
"aa_start": 1176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7280,
"cdna_start": 3626,
"cds_end": null,
"cds_length": 7008,
"cds_start": 3527,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "NM_006445.4",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3527C>T",
"hgvs_p": "p.Ser1176Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000304992.11",
"protein_coding": true,
"protein_id": "NP_006436.3",
"strand": false,
"transcript": "NM_006445.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2335,
"aa_ref": "S",
"aa_start": 1176,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7280,
"cdna_start": 3626,
"cds_end": null,
"cds_length": 7008,
"cds_start": 3527,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000304992.11",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3527C>T",
"hgvs_p": "p.Ser1176Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006445.4",
"protein_coding": true,
"protein_id": "ENSP00000304350.6",
"strand": false,
"transcript": "ENST00000304992.11",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2335,
"aa_ref": "S",
"aa_start": 1176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7445,
"cdna_start": 3793,
"cds_end": null,
"cds_length": 7008,
"cds_start": 3527,
"consequences": [
"missense_variant"
],
"exon_count": 42,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000572621.5",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3527C>T",
"hgvs_p": "p.Ser1176Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000460348.1",
"strand": false,
"transcript": "ENST00000572621.5",
"transcript_support_level": 5
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2335,
"aa_ref": "S",
"aa_start": 1176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7274,
"cdna_start": 3620,
"cds_end": null,
"cds_length": 7008,
"cds_start": 3527,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000883259.1",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3527C>T",
"hgvs_p": "p.Ser1176Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000553318.1",
"strand": false,
"transcript": "ENST00000883259.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2290,
"aa_ref": "S",
"aa_start": 1131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6942,
"cdna_start": 3461,
"cds_end": null,
"cds_length": 6873,
"cds_start": 3392,
"consequences": [
"missense_variant"
],
"exon_count": 42,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000703541.1",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3392C>T",
"hgvs_p": "p.Ser1131Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515363.1",
"strand": false,
"transcript": "ENST00000703541.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2286,
"aa_ref": "S",
"aa_start": 1127,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7086,
"cdna_start": 3464,
"cds_end": null,
"cds_length": 6861,
"cds_start": 3380,
"consequences": [
"missense_variant"
],
"exon_count": 42,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000703540.1",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3380C>T",
"hgvs_p": "p.Ser1127Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515362.1",
"strand": false,
"transcript": "ENST00000703540.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2275,
"aa_ref": "S",
"aa_start": 1176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7073,
"cdna_start": 3622,
"cds_end": null,
"cds_length": 6828,
"cds_start": 3527,
"consequences": [
"missense_variant"
],
"exon_count": 42,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000573725.2",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3527C>T",
"hgvs_p": "p.Ser1176Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000460849.2",
"strand": false,
"transcript": "ENST00000573725.2",
"transcript_support_level": 5
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2271,
"aa_ref": "S",
"aa_start": 1176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7072,
"cdna_start": 3610,
"cds_end": null,
"cds_length": 6816,
"cds_start": 3527,
"consequences": [
"missense_variant"
],
"exon_count": 42,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000912856.1",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3527C>T",
"hgvs_p": "p.Ser1176Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582915.1",
"strand": false,
"transcript": "ENST00000912856.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 2335,
"aa_ref": "S",
"aa_start": 1176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7265,
"cdna_start": 3611,
"cds_end": null,
"cds_length": 7008,
"cds_start": 3527,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_024450537.2",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3527C>T",
"hgvs_p": "p.Ser1176Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024306305.1",
"strand": false,
"transcript": "XM_024450537.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2305,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7191,
"cdna_start": null,
"cds_end": null,
"cds_length": 6918,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 43,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000912855.1",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "c.3447-10C>T",
"hgvs_p": null,
"intron_rank": 22,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582914.1",
"strand": false,
"transcript": "ENST00000912855.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 7212,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 41,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000703538.1",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "n.*3250C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515361.1",
"strand": false,
"transcript": "ENST00000703538.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 7212,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 41,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000703538.1",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "n.*3250C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515361.1",
"strand": false,
"transcript": "ENST00000703538.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 310,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000574217.1",
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"hgvs_c": "n.-78C>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": "ENST00000574217.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs869025267",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 17340,
"gene_symbol": "PRPF8",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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 benign",
"phenotype_combined": "Irido-corneo-trabecular dysgenesis",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.998,
"pos": 1673487,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.692,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07000000029802322,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.07,
"transcript": "NM_006445.4"
}
]
}