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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: 10-70598629-CAG-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=70598629&ref=CAG&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 70598629,
"ref": "CAG",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "ENST00000441259.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.1090_1091delCT",
"hgvs_p": "p.Leu364fs",
"transcript": "NM_001083116.3",
"protein_id": "NP_001076585.1",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 555,
"cds_start": 1090,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1218,
"cdna_end": null,
"cdna_length": 2500,
"mane_select": "ENST00000441259.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.1090_1091delCT",
"hgvs_p": "p.Leu364fs",
"transcript": "ENST00000441259.2",
"protein_id": "ENSP00000398568.1",
"transcript_support_level": 5,
"aa_start": 364,
"aa_end": null,
"aa_length": 555,
"cds_start": 1090,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1218,
"cdna_end": null,
"cdna_length": 2500,
"mane_select": "NM_001083116.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.1090_1091delCT",
"hgvs_p": "p.Leu364fs",
"transcript": "ENST00000373209.2",
"protein_id": "ENSP00000362305.1",
"transcript_support_level": 1,
"aa_start": 364,
"aa_end": null,
"aa_length": 555,
"cds_start": 1090,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1210,
"cdna_end": null,
"cdna_length": 2492,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.1090_1091delCT",
"hgvs_p": "p.Leu364fs",
"transcript": "NM_005041.6",
"protein_id": "NP_005032.2",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 555,
"cds_start": 1090,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1192,
"cdna_end": null,
"cdna_length": 2474,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "c.2419-258_2419-257delAG",
"hgvs_p": null,
"transcript": "ENST00000697571.1",
"protein_id": "ENSP00000513342.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 865,
"cds_start": -4,
"cds_end": null,
"cds_length": 2598,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "c.2263-258_2263-257delAG",
"hgvs_p": null,
"transcript": "ENST00000697573.1",
"protein_id": "ENSP00000513344.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 813,
"cds_start": -4,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "c.2250+34111_2250+34112delAG",
"hgvs_p": null,
"transcript": "ENST00000697572.1",
"protein_id": "ENSP00000513343.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 763,
"cds_start": -4,
"cds_end": null,
"cds_length": 2292,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "c.540-790_540-789delCT",
"hgvs_p": null,
"transcript": "ENST00000638674.1",
"protein_id": "ENSP00000492048.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 232,
"cds_start": -4,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1080,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"hgvs_c": "n.98-790_98-789delCT",
"hgvs_p": null,
"transcript": "ENST00000639390.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 523,
"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": 21,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "n.2723-258_2723-257delAG",
"hgvs_p": null,
"transcript": "ENST00000697577.1",
"protein_id": null,
"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": 3005,
"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": 20,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PALD1",
"gene_hgnc_id": 23530,
"hgvs_c": "n.2567-258_2567-257delAG",
"hgvs_p": null,
"transcript": "ENST00000697578.1",
"protein_id": null,
"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": 3025,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRF1",
"gene_hgnc_id": 9360,
"dbsnp": "rs771552960",
"frequency_reference_population": 0.00001505987,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000150599,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 8.38,
"phylop100way_prediction": "Pathogenic",
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000441259.2",
"gene_symbol": "PRF1",
"hgnc_id": 9360,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.1090_1091delCT",
"hgvs_p": "p.Leu364fs"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000697571.1",
"gene_symbol": "PALD1",
"hgnc_id": 23530,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2419-258_2419-257delAG",
"hgvs_p": null
}
],
"clinvar_disease": " familial, non-Hodgkin,Aplastic anemia,Familial hemophagocytic lymphohistiocytosis,Familial hemophagocytic lymphohistiocytosis 2,Lymphoma",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 O:1",
"phenotype_combined": "Familial hemophagocytic lymphohistiocytosis 2|Aplastic anemia|Aplastic anemia;Lymphoma, non-Hodgkin, familial;Familial hemophagocytic lymphohistiocytosis 2|Familial hemophagocytic lymphohistiocytosis",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}