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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: 4-185508521-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=185508521&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 185508521,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_014476.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.440G>A",
"hgvs_p": "p.Arg147His",
"transcript": "NM_014476.6",
"protein_id": "NP_055291.2",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 364,
"cds_start": 440,
"cds_end": null,
"cds_length": 1095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000284767.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014476.6"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.440G>A",
"hgvs_p": "p.Arg147His",
"transcript": "ENST00000284767.12",
"protein_id": "ENSP00000284767.8",
"transcript_support_level": 5,
"aa_start": 147,
"aa_end": null,
"aa_length": 364,
"cds_start": 440,
"cds_end": null,
"cds_length": 1095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014476.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000284767.12"
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.519-1869G>A",
"hgvs_p": null,
"transcript": "ENST00000284771.7",
"protein_id": "ENSP00000284771.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 316,
"cds_start": null,
"cds_end": null,
"cds_length": 951,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000284771.7"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.162-1869G>A",
"hgvs_p": null,
"transcript": "ENST00000284770.10",
"protein_id": "ENSP00000284770.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 197,
"cds_start": null,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000284770.10"
},
{
"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": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.4162-1869G>A",
"hgvs_p": null,
"transcript": "ENST00000514142.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000514142.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.*58G>A",
"hgvs_p": null,
"transcript": "XM_047450071.1",
"protein_id": "XP_047306027.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 189,
"cds_start": null,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047450071.1"
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.519-1869G>A",
"hgvs_p": null,
"transcript": "NM_001114107.5",
"protein_id": "NP_001107579.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 316,
"cds_start": null,
"cds_end": null,
"cds_length": 951,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001114107.5"
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.399-1869G>A",
"hgvs_p": null,
"transcript": "NM_001257962.2",
"protein_id": "NP_001244891.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 276,
"cds_start": null,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001257962.2"
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.399-1869G>A",
"hgvs_p": null,
"transcript": "ENST00000620787.5",
"protein_id": "ENSP00000481771.2",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 276,
"cds_start": null,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000620787.5"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.162-1869G>A",
"hgvs_p": null,
"transcript": "NM_001257963.2",
"protein_id": "NP_001244892.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 197,
"cds_start": null,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001257963.2"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.*17-1869G>A",
"hgvs_p": null,
"transcript": "XM_047450072.1",
"protein_id": "XP_047306028.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 189,
"cds_start": null,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047450072.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.*159G>A",
"hgvs_p": null,
"transcript": "ENST00000512293.1",
"protein_id": "ENSP00000421972.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000512293.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.*159G>A",
"hgvs_p": null,
"transcript": "ENST00000512293.1",
"protein_id": "ENSP00000421972.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000512293.1"
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.*238-1869G>A",
"hgvs_p": null,
"transcript": "ENST00000505886.5",
"protein_id": "ENSP00000425138.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000505886.5"
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.*707-1869G>A",
"hgvs_p": null,
"transcript": "ENST00000643009.1",
"protein_id": "ENSP00000495411.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000643009.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000249679",
"gene_hgnc_id": 58917,
"hgvs_c": "n.514-18818C>T",
"hgvs_p": null,
"transcript": "ENST00000725791.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000725791.1"
},
{
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.404-1869G>A",
"hgvs_p": null,
"transcript": "NR_047562.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_047562.2"
}
],
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"dbsnp": "rs528843301",
"frequency_reference_population": 0.000016108386,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000143663,
"gnomad_genomes_af": 0.0000328282,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.24964812397956848,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.274,
"revel_prediction": "Benign",
"alphamissense_score": 0.1077,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.217,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_014476.6",
"gene_symbol": "PDLIM3",
"hgnc_id": 20767,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.440G>A",
"hgvs_p": "p.Arg147His"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000725791.1",
"gene_symbol": "ENSG00000249679",
"hgnc_id": 58917,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.514-18818C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Hypertrophic cardiomyopathy,PDLIM3-related disorder,Primary dilated cardiomyopathy,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy|not provided|not specified|PDLIM3-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}