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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: 1-15731198-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=15731198&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 15731198,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000375799.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.2406G>T",
"hgvs_p": "p.Gly802Gly",
"transcript": "NM_015164.4",
"protein_id": "NP_055979.2",
"transcript_support_level": null,
"aa_start": 802,
"aa_end": null,
"aa_length": 1019,
"cds_start": 2406,
"cds_end": null,
"cds_length": 3060,
"cdna_start": 2645,
"cdna_end": null,
"cdna_length": 4134,
"mane_select": "ENST00000375799.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.2406G>T",
"hgvs_p": "p.Gly802Gly",
"transcript": "ENST00000375799.8",
"protein_id": "ENSP00000364956.3",
"transcript_support_level": 1,
"aa_start": 802,
"aa_end": null,
"aa_length": 1019,
"cds_start": 2406,
"cds_end": null,
"cds_length": 3060,
"cdna_start": 2645,
"cdna_end": null,
"cdna_length": 4134,
"mane_select": "NM_015164.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.2445G>T",
"hgvs_p": "p.Gly815Gly",
"transcript": "ENST00000850891.1",
"protein_id": "ENSP00000520968.1",
"transcript_support_level": null,
"aa_start": 815,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2445,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 2585,
"cdna_end": null,
"cdna_length": 4074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.2346G>T",
"hgvs_p": "p.Gly782Gly",
"transcript": "NM_001410755.1",
"protein_id": "NP_001397684.1",
"transcript_support_level": null,
"aa_start": 782,
"aa_end": null,
"aa_length": 999,
"cds_start": 2346,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 2585,
"cdna_end": null,
"cdna_length": 4074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.2346G>T",
"hgvs_p": "p.Gly782Gly",
"transcript": "ENST00000375793.3",
"protein_id": "ENSP00000364950.2",
"transcript_support_level": 5,
"aa_start": 782,
"aa_end": null,
"aa_length": 999,
"cds_start": 2346,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 3022,
"cdna_end": null,
"cdna_length": 4511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.2283G>T",
"hgvs_p": "p.Gly761Gly",
"transcript": "ENST00000642363.1",
"protein_id": "ENSP00000494591.1",
"transcript_support_level": null,
"aa_start": 761,
"aa_end": null,
"aa_length": 978,
"cds_start": 2283,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 2286,
"cdna_end": null,
"cdna_length": 3775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.2445G>T",
"hgvs_p": "p.Gly815Gly",
"transcript": "XM_017000757.1",
"protein_id": "XP_016856246.1",
"transcript_support_level": null,
"aa_start": 815,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2445,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 2540,
"cdna_end": null,
"cdna_length": 4029,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.2385G>T",
"hgvs_p": "p.Gly795Gly",
"transcript": "XM_017000758.1",
"protein_id": "XP_016856247.1",
"transcript_support_level": null,
"aa_start": 795,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2385,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 2480,
"cdna_end": null,
"cdna_length": 3969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "c.1797G>T",
"hgvs_p": "p.Gly599Gly",
"transcript": "XM_005245791.5",
"protein_id": "XP_005245848.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 816,
"cds_start": 1797,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1905,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.283G>T",
"hgvs_p": null,
"transcript": "ENST00000477849.1",
"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": 1057,
"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": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*1414G>T",
"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": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*1856G>T",
"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": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*2041G>T",
"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": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*1414G>T",
"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": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*1856G>T",
"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": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM2",
"gene_hgnc_id": 29131,
"hgvs_c": "n.*2041G>T",
"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": 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.211+1189C>A",
"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.66+1189C>A",
"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.66+1189C>A",
"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": "rs116565708",
"frequency_reference_population": 0.00016093218,
"hom_count_reference_population": 1,
"allele_count_reference_population": 257,
"gnomad_exomes_af": 0.0000872146,
"gnomad_genomes_af": 0.000860517,
"gnomad_exomes_ac": 126,
"gnomad_genomes_ac": 131,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.657,
"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": -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": "ENST00000375799.8",
"gene_symbol": "PLEKHM2",
"hgnc_id": 29131,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2406G>T",
"hgvs_p": "p.Gly802Gly"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000453804.1",
"gene_symbol": "ENSG00000237938",
"hgnc_id": 58402,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.211+1189C>A",
"hgvs_p": null
}
],
"clinvar_disease": " Recessive,Dilated Cardiomyopathy,PLEKHM2-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Dilated Cardiomyopathy, Recessive|PLEKHM2-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}