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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: 19-54128716-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=54128716&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PRPF31",
"hgnc_id": 15446,
"hgvs_c": "c.1146+339G>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_015629.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 6804,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.95,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.949999988079071,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1833,
"cdna_start": null,
"cds_end": null,
"cds_length": 1500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_015629.4",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1146+339G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000321030.9",
"protein_coding": true,
"protein_id": "NP_056444.3",
"strand": true,
"transcript": "NM_015629.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1833,
"cdna_start": null,
"cds_end": null,
"cds_length": 1500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000321030.9",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1146+339G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015629.4",
"protein_coding": true,
"protein_id": "ENSP00000324122.4",
"strand": true,
"transcript": "ENST00000321030.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 532,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1936,
"cdna_start": null,
"cds_end": null,
"cds_length": 1599,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000951323.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1245+339G>A",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621382.1",
"strand": true,
"transcript": "ENST00000951323.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 530,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1915,
"cdna_start": null,
"cds_end": null,
"cds_length": 1593,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000861422.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1239+339G>A",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531481.1",
"strand": true,
"transcript": "ENST00000861422.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 529,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1904,
"cdna_start": null,
"cds_end": null,
"cds_length": 1590,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000929489.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1236+339G>A",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599548.1",
"strand": true,
"transcript": "ENST00000929489.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 522,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1887,
"cdna_start": null,
"cds_end": null,
"cds_length": 1569,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000861423.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1147-21G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531482.1",
"strand": true,
"transcript": "ENST00000861423.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 513,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1870,
"cdna_start": null,
"cds_end": null,
"cds_length": 1542,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000861421.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1188+339G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531480.1",
"strand": true,
"transcript": "ENST00000861421.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 511,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1850,
"cdna_start": null,
"cds_end": null,
"cds_length": 1536,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000861424.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1182+339G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531483.1",
"strand": true,
"transcript": "ENST00000861424.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1856,
"cdna_start": null,
"cds_end": null,
"cds_length": 1500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000861425.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1146+339G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531484.1",
"strand": true,
"transcript": "ENST00000861425.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 498,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1836,
"cdna_start": null,
"cds_end": null,
"cds_length": 1497,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000929488.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1143+339G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599547.1",
"strand": true,
"transcript": "ENST00000929488.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 493,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1767,
"cdna_start": null,
"cds_end": null,
"cds_length": 1482,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000391755.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1128+339G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000375635.1",
"strand": true,
"transcript": "ENST00000391755.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 491,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2269,
"cdna_start": null,
"cds_end": null,
"cds_length": 1476,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000419967.5",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1146+339G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000405166.2",
"strand": true,
"transcript": "ENST00000419967.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 257,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1087,
"cdna_start": null,
"cds_end": null,
"cds_length": 774,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000929490.1",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.421-341G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599549.1",
"strand": true,
"transcript": "ENST00000929490.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1863,
"cdna_start": null,
"cds_end": null,
"cds_length": 1500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_006723137.5",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "c.1146+339G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006723200.1",
"strand": true,
"transcript": "XM_006723137.5",
"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": 1837,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000466404.5",
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"hgvs_c": "n.1120+339G>A",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000466404.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs2556367",
"effect": "intron_variant",
"frequency_reference_population": 0.04473608,
"gene_hgnc_id": 15446,
"gene_symbol": "PRPF31",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 6804,
"gnomad_genomes_af": 0.0447361,
"gnomad_genomes_homalt": 196,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 196,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.497,
"pos": 54128716,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_015629.4"
}
]
}