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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-72581017-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=72581017&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 72581017,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_002637.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3657C>T",
"hgvs_p": "p.Ile1219Ile",
"transcript": "NM_002637.4",
"protein_id": "NP_002628.2",
"transcript_support_level": null,
"aa_start": 1219,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3657,
"cds_end": null,
"cds_length": 3672,
"cdna_start": 4083,
"cdna_end": null,
"cdna_length": 6286,
"mane_select": "ENST00000373542.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3657C>T",
"hgvs_p": "p.Ile1219Ile",
"transcript": "ENST00000373542.9",
"protein_id": "ENSP00000362643.4",
"transcript_support_level": 1,
"aa_start": 1219,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3657,
"cds_end": null,
"cds_length": 3672,
"cdna_start": 4083,
"cdna_end": null,
"cdna_length": 6286,
"mane_select": "NM_002637.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3618C>T",
"hgvs_p": "p.Ile1206Ile",
"transcript": "ENST00000339490.7",
"protein_id": "ENSP00000342469.3",
"transcript_support_level": 1,
"aa_start": 1206,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3618,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3919,
"cdna_end": null,
"cdna_length": 6121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3441C>T",
"hgvs_p": "p.Ile1147Ile",
"transcript": "ENST00000541944.5",
"protein_id": "ENSP00000441251.1",
"transcript_support_level": 1,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3441,
"cds_end": null,
"cds_length": 3456,
"cdna_start": 3742,
"cdna_end": null,
"cdna_length": 5944,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3708C>T",
"hgvs_p": "p.Ile1236Ile",
"transcript": "NM_001431068.1",
"protein_id": "NP_001417997.1",
"transcript_support_level": null,
"aa_start": 1236,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3708,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 4134,
"cdna_end": null,
"cdna_length": 6337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3708C>T",
"hgvs_p": "p.Ile1236Ile",
"transcript": "ENST00000373539.3",
"protein_id": "ENSP00000362640.3",
"transcript_support_level": 5,
"aa_start": 1236,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3708,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 4086,
"cdna_end": null,
"cdna_length": 4476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3618C>T",
"hgvs_p": "p.Ile1206Ile",
"transcript": "NM_001122670.2",
"protein_id": "NP_001116142.1",
"transcript_support_level": null,
"aa_start": 1206,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3618,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 4044,
"cdna_end": null,
"cdna_length": 6247,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3618C>T",
"hgvs_p": "p.Ile1206Ile",
"transcript": "NM_001440787.1",
"protein_id": "NP_001427716.1",
"transcript_support_level": null,
"aa_start": 1206,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3618,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3935,
"cdna_end": null,
"cdna_length": 6138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3531C>T",
"hgvs_p": "p.Ile1177Ile",
"transcript": "ENST00000373545.7",
"protein_id": "ENSP00000362646.3",
"transcript_support_level": 5,
"aa_start": 1177,
"aa_end": null,
"aa_length": 1181,
"cds_start": 3531,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 3970,
"cdna_end": null,
"cdna_length": 6173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3441C>T",
"hgvs_p": "p.Ile1147Ile",
"transcript": "NM_001172436.2",
"protein_id": "NP_001165907.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3441,
"cds_end": null,
"cds_length": 3456,
"cdna_start": 3867,
"cdna_end": null,
"cdna_length": 6070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3441C>T",
"hgvs_p": "p.Ile1147Ile",
"transcript": "NM_001440788.1",
"protein_id": "NP_001427717.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3441,
"cds_end": null,
"cds_length": 3456,
"cdna_start": 3758,
"cdna_end": null,
"cdna_length": 5961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3657C>T",
"hgvs_p": "p.Ile1219Ile",
"transcript": "XM_047442160.1",
"protein_id": "XP_047298116.1",
"transcript_support_level": null,
"aa_start": 1219,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3657,
"cds_end": null,
"cds_length": 3672,
"cdna_start": 3974,
"cdna_end": null,
"cdna_length": 6177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3480C>T",
"hgvs_p": "p.Ile1160Ile",
"transcript": "XM_006724661.3",
"protein_id": "XP_006724724.1",
"transcript_support_level": null,
"aa_start": 1160,
"aa_end": null,
"aa_length": 1164,
"cds_start": 3480,
"cds_end": null,
"cds_length": 3495,
"cdna_start": 3906,
"cdna_end": null,
"cdna_length": 6109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"dbsnp": "rs782049839",
"frequency_reference_population": 0.00000578764,
"hom_count_reference_population": 2,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000546791,
"gnomad_genomes_af": 0.00000891568,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"computational_prediction_selected": "Benign",
"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": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.555,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_002637.4",
"gene_symbol": "PHKA1",
"hgnc_id": 8925,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.3657C>T",
"hgvs_p": "p.Ile1219Ile"
}
],
"clinvar_disease": "Glycogen storage disease IXd",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Glycogen storage disease IXd",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}