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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: 10-3103861-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=3103861&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 3103861,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000381125.9",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.537C>A",
"hgvs_p": "p.Cys179*",
"transcript": "NM_002627.5",
"protein_id": "NP_002618.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 784,
"cds_start": 537,
"cds_end": null,
"cds_length": 2355,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 2626,
"mane_select": "ENST00000381125.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.537C>A",
"hgvs_p": "p.Cys179*",
"transcript": "ENST00000381125.9",
"protein_id": "ENSP00000370517.4",
"transcript_support_level": 1,
"aa_start": 179,
"aa_end": null,
"aa_length": 784,
"cds_start": 537,
"cds_end": null,
"cds_length": 2355,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 2626,
"mane_select": "NM_002627.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.537C>A",
"hgvs_p": "p.Cys179*",
"transcript": "NM_001410880.1",
"protein_id": "NP_001397809.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 835,
"cds_start": 537,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 2779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.537C>A",
"hgvs_p": "p.Cys179*",
"transcript": "ENST00000699222.1",
"protein_id": "ENSP00000514216.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 835,
"cds_start": 537,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 2819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.513C>A",
"hgvs_p": "p.Cys171*",
"transcript": "NM_001242339.2",
"protein_id": "NP_001229268.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 776,
"cds_start": 513,
"cds_end": null,
"cds_length": 2331,
"cdna_start": 737,
"cdna_end": null,
"cdna_length": 2778,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.456C>A",
"hgvs_p": "p.Cys152*",
"transcript": "NM_001323067.2",
"protein_id": "NP_001309996.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 757,
"cds_start": 456,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 476,
"cdna_end": null,
"cdna_length": 2517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Cys141*",
"transcript": "NM_001323071.2",
"protein_id": "NP_001310000.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 746,
"cds_start": 423,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 701,
"cdna_end": null,
"cdna_length": 2742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Cys141*",
"transcript": "NM_001323072.2",
"protein_id": "NP_001310001.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 746,
"cds_start": 423,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 836,
"cdna_end": null,
"cdna_length": 2877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Cys141*",
"transcript": "NM_001345944.1",
"protein_id": "NP_001332873.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 746,
"cds_start": 423,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 2667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Cys141*",
"transcript": "ENST00000381075.7",
"protein_id": "ENSP00000370465.3",
"transcript_support_level": 2,
"aa_start": 141,
"aa_end": null,
"aa_length": 746,
"cds_start": 423,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 704,
"cdna_end": null,
"cdna_length": 2741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Cys141*",
"transcript": "ENST00000676796.1",
"protein_id": "ENSP00000503786.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 746,
"cds_start": 423,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 722,
"cdna_end": null,
"cdna_length": 2759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.537C>A",
"hgvs_p": "p.Cys179*",
"transcript": "NM_001323068.2",
"protein_id": "NP_001309997.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 733,
"cds_start": 537,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 2473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.30C>A",
"hgvs_p": "p.Cys10*",
"transcript": "NM_001323069.2",
"protein_id": "NP_001309998.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 615,
"cds_start": 30,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 580,
"cdna_end": null,
"cdna_length": 2621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Cys141*",
"transcript": "ENST00000407806.2",
"protein_id": "ENSP00000385880.2",
"transcript_support_level": 5,
"aa_start": 141,
"aa_end": null,
"aa_length": 209,
"cds_start": 423,
"cds_end": null,
"cds_length": 632,
"cdna_start": 496,
"cdna_end": null,
"cdna_length": 705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Cys141*",
"transcript": "XM_006717449.2",
"protein_id": "XP_006717512.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 797,
"cds_start": 423,
"cds_end": null,
"cds_length": 2394,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 2823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.423C>A",
"hgvs_p": "p.Cys141*",
"transcript": "XM_047425350.1",
"protein_id": "XP_047281306.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 797,
"cds_start": 423,
"cds_end": null,
"cds_length": 2394,
"cdna_start": 836,
"cdna_end": null,
"cdna_length": 3033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "c.537C>A",
"hgvs_p": "p.Cys179*",
"transcript": "XM_005252466.5",
"protein_id": "XP_005252523.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 784,
"cds_start": 537,
"cds_end": null,
"cds_length": 2355,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 2629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "n.582C>A",
"hgvs_p": null,
"transcript": "ENST00000421751.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "n.*344C>A",
"hgvs_p": null,
"transcript": "ENST00000678089.1",
"protein_id": "ENSP00000503212.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "n.*344C>A",
"hgvs_p": null,
"transcript": "ENST00000678089.1",
"protein_id": "ENSP00000503212.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"hgvs_c": "n.341-1254C>A",
"hgvs_p": null,
"transcript": "ENST00000678206.1",
"protein_id": "ENSP00000504635.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PFKP",
"gene_hgnc_id": 8878,
"dbsnp": "rs61760977",
"frequency_reference_population": 6.84148e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84148e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.27000001072883606,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": -0.104,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000381125.9",
"gene_symbol": "PFKP",
"hgnc_id": 8878,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.537C>A",
"hgvs_p": "p.Cys179*"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}