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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: X-72599841-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=72599841&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 72599841,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "NM_002637.4",
"consequences": [
{
"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": 32,
"intron_rank": 28,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3072+2150T>C",
"hgvs_p": null,
"transcript": "NM_002637.4",
"protein_id": "NP_002628.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1223,
"cds_start": -4,
"cds_end": null,
"cds_length": 3672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6286,
"mane_select": "ENST00000373542.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 28,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3072+2150T>C",
"hgvs_p": null,
"transcript": "ENST00000373542.9",
"protein_id": "ENSP00000362643.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1223,
"cds_start": -4,
"cds_end": null,
"cds_length": 3672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6286,
"mane_select": "NM_002637.4",
"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": 31,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3033+2317T>C",
"hgvs_p": null,
"transcript": "ENST00000339490.7",
"protein_id": "ENSP00000342469.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1210,
"cds_start": -4,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6121,
"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": 30,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.2856+2317T>C",
"hgvs_p": null,
"transcript": "ENST00000541944.5",
"protein_id": "ENSP00000441251.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1151,
"cds_start": -4,
"cds_end": null,
"cds_length": 3456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5944,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3098T>C",
"hgvs_p": "p.Ile1033Thr",
"transcript": "NM_001431068.1",
"protein_id": "NP_001417997.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3098,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 3524,
"cdna_end": null,
"cdna_length": 6337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3098T>C",
"hgvs_p": "p.Ile1033Thr",
"transcript": "ENST00000373539.3",
"protein_id": "ENSP00000362640.3",
"transcript_support_level": 5,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3098,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 3476,
"cdna_end": null,
"cdna_length": 4476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.2921T>C",
"hgvs_p": "p.Ile974Thr",
"transcript": "ENST00000373545.7",
"protein_id": "ENSP00000362646.3",
"transcript_support_level": 5,
"aa_start": 974,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2921,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 3360,
"cdna_end": null,
"cdna_length": 6173,
"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": 31,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3033+2317T>C",
"hgvs_p": null,
"transcript": "NM_001122670.2",
"protein_id": "NP_001116142.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1210,
"cds_start": -4,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6247,
"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": 32,
"intron_rank": 28,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3033+2317T>C",
"hgvs_p": null,
"transcript": "NM_001440787.1",
"protein_id": "NP_001427716.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1210,
"cds_start": -4,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6138,
"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": 30,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.2856+2317T>C",
"hgvs_p": null,
"transcript": "NM_001172436.2",
"protein_id": "NP_001165907.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1151,
"cds_start": -4,
"cds_end": null,
"cds_length": 3456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6070,
"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": 31,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.2856+2317T>C",
"hgvs_p": null,
"transcript": "NM_001440788.1",
"protein_id": "NP_001427717.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1151,
"cds_start": -4,
"cds_end": null,
"cds_length": 3456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5961,
"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": 33,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3072+2150T>C",
"hgvs_p": null,
"transcript": "XM_047442160.1",
"protein_id": "XP_047298116.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1223,
"cds_start": -4,
"cds_end": null,
"cds_length": 3672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6177,
"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": 31,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.2895+2150T>C",
"hgvs_p": null,
"transcript": "XM_006724661.3",
"protein_id": "XP_006724724.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1164,
"cds_start": -4,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"dbsnp": "rs7054230",
"frequency_reference_population": 0.11468388,
"hom_count_reference_population": 30057,
"allele_count_reference_population": 62972,
"gnomad_exomes_af": 0.110068,
"gnomad_genomes_af": 0.133005,
"gnomad_exomes_ac": 48276,
"gnomad_genomes_ac": 14696,
"gnomad_exomes_homalt": 7200,
"gnomad_genomes_homalt": 1674,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000009342983503302094,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.073,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.021,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_002637.4",
"gene_symbol": "PHKA1",
"hgnc_id": 8925,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.3072+2150T>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}