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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: 4-185523446-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=185523446&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 185523446,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000284767.12",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg",
"transcript": "NM_014476.6",
"protein_id": "NP_055291.2",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 364,
"cds_start": 246,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 2802,
"mane_select": "ENST00000284767.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg",
"transcript": "ENST00000284767.12",
"protein_id": "ENSP00000284767.8",
"transcript_support_level": 5,
"aa_start": 82,
"aa_end": null,
"aa_length": 364,
"cds_start": 246,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 2802,
"mane_select": "NM_014476.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg",
"transcript": "ENST00000284771.7",
"protein_id": "ENSP00000284771.6",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 316,
"cds_start": 246,
"cds_end": null,
"cds_length": 951,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 2658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.303G>A",
"hgvs_p": null,
"transcript": "ENST00000504011.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.94-9109G>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": -4,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg",
"transcript": "NM_001114107.5",
"protein_id": "NP_001107579.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 316,
"cds_start": 246,
"cds_end": null,
"cds_length": 951,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 2658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg",
"transcript": "NM_001257962.2",
"protein_id": "NP_001244891.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 276,
"cds_start": 246,
"cds_end": null,
"cds_length": 831,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 2538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg",
"transcript": "ENST00000620787.5",
"protein_id": "ENSP00000481771.2",
"transcript_support_level": 4,
"aa_start": 82,
"aa_end": null,
"aa_length": 276,
"cds_start": 246,
"cds_end": null,
"cds_length": 831,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 1108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg",
"transcript": "XM_047450071.1",
"protein_id": "XP_047306027.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 189,
"cds_start": 246,
"cds_end": null,
"cds_length": 570,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg",
"transcript": "XM_047450072.1",
"protein_id": "XP_047306028.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 189,
"cds_start": 246,
"cds_end": null,
"cds_length": 570,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.94G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.94G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.104G>A",
"hgvs_p": null,
"transcript": "ENST00000512380.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 764,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.319G>A",
"hgvs_p": null,
"transcript": "ENST00000515261.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 622,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.234G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.319G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "c.94-9109G>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": -4,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2301,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"hgvs_c": "n.318+1574G>A",
"hgvs_p": null,
"transcript": "ENST00000504355.5",
"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": 510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": null,
"hgvs_c": "n.514-3893C>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDLIM3",
"gene_hgnc_id": 20767,
"dbsnp": "rs200354645",
"frequency_reference_population": 0.00016385302,
"hom_count_reference_population": 1,
"allele_count_reference_population": 260,
"gnomad_exomes_af": 0.000166607,
"gnomad_genomes_af": 0.000137911,
"gnomad_exomes_ac": 239,
"gnomad_genomes_ac": 21,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1572812795639038,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.15600000321865082,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.052,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0061675186448941,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000284767.12",
"gene_symbol": "PDLIM3",
"hgnc_id": 20767,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.246G>A",
"hgvs_p": "p.Arg82Arg"
},
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000725791.1",
"gene_symbol": "ENSG00000249679",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.514-3893C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Hypertrophic cardiomyopathy,Primary dilated cardiomyopathy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy|not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}