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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: 1-15727122-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=15727122&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 15727122,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000375799.8",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.1050C>A",
"hgvs_p": "p.Asp350Glu",
"transcript": "NM_015164.4",
"protein_id": "NP_055979.2",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 1019,
"cds_start": 1050,
"cds_end": null,
"cds_length": 3060,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 4134,
"mane_select": "ENST00000375799.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.1050C>A",
"hgvs_p": "p.Asp350Glu",
"transcript": "ENST00000375799.8",
"protein_id": "ENSP00000364956.3",
"transcript_support_level": 1,
"aa_start": 350,
"aa_end": null,
"aa_length": 1019,
"cds_start": 1050,
"cds_end": null,
"cds_length": 3060,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 4134,
"mane_select": "NM_015164.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.1089C>A",
"hgvs_p": "p.Asp363Glu",
"transcript": "ENST00000850891.1",
"protein_id": "ENSP00000520968.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 1032,
"cds_start": 1089,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 4074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.990C>A",
"hgvs_p": "p.Asp330Glu",
"transcript": "NM_001410755.1",
"protein_id": "NP_001397684.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 999,
"cds_start": 990,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 4074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.990C>A",
"hgvs_p": "p.Asp330Glu",
"transcript": "ENST00000375793.3",
"protein_id": "ENSP00000364950.2",
"transcript_support_level": 5,
"aa_start": 330,
"aa_end": null,
"aa_length": 999,
"cds_start": 990,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 1666,
"cdna_end": null,
"cdna_length": 4511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.1089C>A",
"hgvs_p": "p.Asp363Glu",
"transcript": "XM_017000757.1",
"protein_id": "XP_016856246.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 1032,
"cds_start": 1089,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 4029,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.1029C>A",
"hgvs_p": "p.Asp343Glu",
"transcript": "XM_017000758.1",
"protein_id": "XP_016856247.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 1012,
"cds_start": 1029,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 1124,
"cdna_end": null,
"cdna_length": 3969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.441C>A",
"hgvs_p": "p.Asp147Glu",
"transcript": "XM_005245791.5",
"protein_id": "XP_005245848.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 816,
"cds_start": 441,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 549,
"cdna_end": null,
"cdna_length": 3394,
"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": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*58C>A",
"hgvs_p": null,
"transcript": "ENST00000718275.1",
"protein_id": "ENSP00000520713.1",
"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": 4126,
"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": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*500C>A",
"hgvs_p": null,
"transcript": "ENST00000718276.2",
"protein_id": "ENSP00000520714.2",
"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": 4247,
"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": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*685C>A",
"hgvs_p": null,
"transcript": "ENST00000850912.1",
"protein_id": "ENSP00000520995.1",
"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": 4024,
"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": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*58C>A",
"hgvs_p": null,
"transcript": "ENST00000718275.1",
"protein_id": "ENSP00000520713.1",
"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": 4126,
"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": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*500C>A",
"hgvs_p": null,
"transcript": "ENST00000718276.2",
"protein_id": "ENSP00000520714.2",
"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": 4247,
"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": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*685C>A",
"hgvs_p": null,
"transcript": "ENST00000850912.1",
"protein_id": "ENSP00000520995.1",
"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": 4024,
"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": 9,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.996+54C>A",
"hgvs_p": null,
"transcript": "ENST00000642363.1",
"protein_id": "ENSP00000494591.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 978,
"cds_start": -4,
"cds_end": null,
"cds_length": 2937,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3775,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000237938",
"gene_hgnc_id": 58402,
"hgvs_c": "n.212-3835G>T",
"hgvs_p": null,
"transcript": "ENST00000453804.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 645,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000237938",
"gene_hgnc_id": 58402,
"hgvs_c": "n.67-1250G>T",
"hgvs_p": null,
"transcript": "ENST00000615472.1",
"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": 755,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000237938",
"gene_hgnc_id": 58402,
"hgvs_c": "n.67-3769G>T",
"hgvs_p": null,
"transcript": "ENST00000623689.3",
"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": 684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"dbsnp": "rs370961093",
"frequency_reference_population": 6.9784744e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.97847e-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": 0.037596166133880615,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.0891,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.886,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000375799.8",
"gene_symbol": "PLEKHM2",
"hgnc_id": 29131,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1050C>A",
"hgvs_p": "p.Asp350Glu"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000453804.1",
"gene_symbol": "ENSG00000237938",
"hgnc_id": 58402,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.212-3835G>T",
"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
}