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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: 1-15733909-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=15733909&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PLEKHM2",
"hgnc_id": 29131,
"hgvs_c": "c.3035G>A",
"hgvs_p": "p.Arg1012Gln",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -1,
"transcript": "NM_015164.4",
"verdict": "Likely_benign"
},
{
"benign_score": 1,
"criteria": [
"BP4"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000237938",
"hgnc_id": 58402,
"hgvs_c": "n.37-1348C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -1,
"transcript": "ENST00000453804.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_score": -1,
"allele_count_reference_population": 307,
"alphamissense_prediction": null,
"alphamissense_score": 0.5174,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.12,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " Recessive,Dilated Cardiomyopathy,PLEKHM2-related disorder,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.3072091042995453,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1019,
"aa_ref": "R",
"aa_start": 1012,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4134,
"cdna_start": 3274,
"cds_end": null,
"cds_length": 3060,
"cds_start": 3035,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_015164.4",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3035G>A",
"hgvs_p": "p.Arg1012Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000375799.8",
"protein_coding": true,
"protein_id": "NP_055979.2",
"strand": true,
"transcript": "NM_015164.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1019,
"aa_ref": "R",
"aa_start": 1012,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4134,
"cdna_start": 3274,
"cds_end": null,
"cds_length": 3060,
"cds_start": 3035,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000375799.8",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3035G>A",
"hgvs_p": "p.Arg1012Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015164.4",
"protein_coding": true,
"protein_id": "ENSP00000364956.3",
"strand": true,
"transcript": "ENST00000375799.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1055,
"aa_ref": "R",
"aa_start": 1048,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4015,
"cdna_start": 3157,
"cds_end": null,
"cds_length": 3168,
"cds_start": 3143,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000957356.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3143G>A",
"hgvs_p": "p.Arg1048Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627415.1",
"strand": true,
"transcript": "ENST00000957356.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1034,
"aa_ref": "R",
"aa_start": 1027,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4189,
"cdna_start": 3332,
"cds_end": null,
"cds_length": 3105,
"cds_start": 3080,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000957353.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3080G>A",
"hgvs_p": "p.Arg1027Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627412.1",
"strand": true,
"transcript": "ENST00000957353.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1032,
"aa_ref": "R",
"aa_start": 1025,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4074,
"cdna_start": 3214,
"cds_end": null,
"cds_length": 3099,
"cds_start": 3074,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000850891.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3074G>A",
"hgvs_p": "p.Arg1025Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000520968.1",
"strand": true,
"transcript": "ENST00000850891.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1017,
"aa_ref": "R",
"aa_start": 1010,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4078,
"cdna_start": 3218,
"cds_end": null,
"cds_length": 3054,
"cds_start": 3029,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000957355.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3029G>A",
"hgvs_p": "p.Arg1010Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627414.1",
"strand": true,
"transcript": "ENST00000957355.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1015,
"aa_ref": "R",
"aa_start": 1008,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3892,
"cdna_start": 3061,
"cds_end": null,
"cds_length": 3048,
"cds_start": 3023,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000957357.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3023G>A",
"hgvs_p": "p.Arg1008Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627416.1",
"strand": true,
"transcript": "ENST00000957357.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 999,
"aa_ref": "R",
"aa_start": 992,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4074,
"cdna_start": 3214,
"cds_end": null,
"cds_length": 3000,
"cds_start": 2975,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_001410755.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.2975G>A",
"hgvs_p": "p.Arg992Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397684.1",
"strand": true,
"transcript": "NM_001410755.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 999,
"aa_ref": "R",
"aa_start": 992,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4511,
"cdna_start": 3651,
"cds_end": null,
"cds_length": 3000,
"cds_start": 2975,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000375793.3",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.2975G>A",
"hgvs_p": "p.Arg992Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000364950.2",
"strand": true,
"transcript": "ENST00000375793.3",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 978,
"aa_ref": "R",
"aa_start": 971,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3775,
"cdna_start": 2915,
"cds_end": null,
"cds_length": 2937,
"cds_start": 2912,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000642363.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.2912G>A",
"hgvs_p": "p.Arg971Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000494591.1",
"strand": true,
"transcript": "ENST00000642363.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 874,
"aa_ref": "R",
"aa_start": 867,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3703,
"cdna_start": 2843,
"cds_end": null,
"cds_length": 2625,
"cds_start": 2600,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000957354.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.2600G>A",
"hgvs_p": "p.Arg867Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627413.1",
"strand": true,
"transcript": "ENST00000957354.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1032,
"aa_ref": "R",
"aa_start": 1025,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4029,
"cdna_start": 3169,
"cds_end": null,
"cds_length": 3099,
"cds_start": 3074,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_017000757.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3074G>A",
"hgvs_p": "p.Arg1025Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856246.1",
"strand": true,
"transcript": "XM_017000757.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "R",
"aa_start": 1005,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3969,
"cdna_start": 3109,
"cds_end": null,
"cds_length": 3039,
"cds_start": 3014,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_017000758.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.3014G>A",
"hgvs_p": "p.Arg1005Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856247.1",
"strand": true,
"transcript": "XM_017000758.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 816,
"aa_ref": "R",
"aa_start": 809,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3394,
"cdna_start": 2534,
"cds_end": null,
"cds_length": 2451,
"cds_start": 2426,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_005245791.5",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "c.2426G>A",
"hgvs_p": "p.Arg809Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005245848.1",
"strand": true,
"transcript": "XM_005245791.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1057,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000477849.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "n.851G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000477849.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4126,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000718275.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "n.*2043G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000520713.1",
"strand": true,
"transcript": "ENST00000718275.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4247,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000718276.2",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "n.*2485G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000520714.2",
"strand": true,
"transcript": "ENST00000718276.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4024,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000850912.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "n.*2670G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000520995.1",
"strand": true,
"transcript": "ENST00000850912.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4126,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000718275.1",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "n.*2043G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000520713.1",
"strand": true,
"transcript": "ENST00000718275.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4247,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000718276.2",
"gene_hgnc_id": 29131,
"gene_symbol": "PLEKHM2",
"hgvs_c": "n.*2485G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000520714.2",
"strand": true,
"transcript": "ENST00000718276.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
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{
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],
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}
]
}