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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: 19-40380712-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40380712&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 40380712,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000291823.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIPK4",
"gene_hgnc_id": 19007,
"hgvs_c": "c.1279G>T",
"hgvs_p": "p.Asp427Tyr",
"transcript": "NM_144685.5",
"protein_id": "NP_653286.2",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 616,
"cds_start": 1279,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1558,
"cdna_end": null,
"cdna_length": 2446,
"mane_select": "ENST00000291823.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIPK4",
"gene_hgnc_id": 19007,
"hgvs_c": "c.1279G>T",
"hgvs_p": "p.Asp427Tyr",
"transcript": "ENST00000291823.3",
"protein_id": "ENSP00000291823.1",
"transcript_support_level": 1,
"aa_start": 427,
"aa_end": null,
"aa_length": 616,
"cds_start": 1279,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1558,
"cdna_end": null,
"cdna_length": 2446,
"mane_select": "NM_144685.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*2539C>A",
"hgvs_p": null,
"transcript": "ENST00000700616.1",
"protein_id": "ENSP00000515107.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*386C>A",
"hgvs_p": null,
"transcript": "ENST00000700619.1",
"protein_id": "ENSP00000515110.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*2539C>A",
"hgvs_p": null,
"transcript": "ENST00000700621.1",
"protein_id": "ENSP00000515112.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*2539C>A",
"hgvs_p": null,
"transcript": "ENST00000700623.1",
"protein_id": "ENSP00000515113.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*2539C>A",
"hgvs_p": null,
"transcript": "ENST00000700625.1",
"protein_id": "ENSP00000515115.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*2539C>A",
"hgvs_p": null,
"transcript": "ENST00000700626.1",
"protein_id": "ENSP00000515116.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5062,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*2539C>A",
"hgvs_p": null,
"transcript": "ENST00000700628.1",
"protein_id": "ENSP00000515117.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*2539C>A",
"hgvs_p": null,
"transcript": "ENST00000700630.1",
"protein_id": "ENSP00000515118.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5762,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*386C>A",
"hgvs_p": null,
"transcript": "ENST00000700632.1",
"protein_id": "ENSP00000515120.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*2539C>A",
"hgvs_p": null,
"transcript": "ENST00000700624.1",
"protein_id": "ENSP00000515114.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 468,
"cds_start": -4,
"cds_end": null,
"cds_length": 1407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4664,
"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": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*50+2489C>A",
"hgvs_p": null,
"transcript": "ENST00000700620.1",
"protein_id": "ENSP00000515111.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1806,
"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": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*50+2489C>A",
"hgvs_p": null,
"transcript": "ENST00000700633.1",
"protein_id": "ENSP00000515121.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1961,
"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": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.*50+2489C>A",
"hgvs_p": null,
"transcript": "ENST00000700634.1",
"protein_id": "ENSP00000515122.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 490,
"cds_start": -4,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HIPK4",
"gene_hgnc_id": 19007,
"dbsnp": "rs193920880",
"frequency_reference_population": 6.8410776e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84108e-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": 0.7180908918380737,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.484,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1732,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.372,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000291823.3",
"gene_symbol": "HIPK4",
"hgnc_id": 19007,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1279G>T",
"hgvs_p": "p.Asp427Tyr"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000700616.1",
"gene_symbol": "PLD3",
"hgnc_id": 17158,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.*2539C>A",
"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
}