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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: 2-218271546-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218271546&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PNKD",
"hgnc_id": 9153,
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_015488.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.23,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.46,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases,Paroxysmal nonkinesigenic dyskinesia",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.7199677228927612,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 385,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2987,
"cdna_start": 250,
"cds_end": null,
"cds_length": 1158,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_015488.5",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000273077.9",
"protein_coding": true,
"protein_id": "NP_056303.3",
"strand": true,
"transcript": "NM_015488.5",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 385,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2987,
"cdna_start": 250,
"cds_end": null,
"cds_length": 1158,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000273077.9",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015488.5",
"protein_coding": true,
"protein_id": "ENSP00000273077.4",
"strand": true,
"transcript": "ENST00000273077.9",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 142,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 758,
"cdna_start": 377,
"cds_end": null,
"cds_length": 429,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000248451.7",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000248451.3",
"strand": true,
"transcript": "ENST00000248451.7",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 424,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3100,
"cdna_start": 255,
"cds_end": null,
"cds_length": 1275,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000685415.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510415.1",
"strand": true,
"transcript": "ENST00000685415.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 418,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3086,
"cdna_start": 250,
"cds_end": null,
"cds_length": 1257,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000901530.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000571589.1",
"strand": true,
"transcript": "ENST00000901530.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 395,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3011,
"cdna_start": 260,
"cds_end": null,
"cds_length": 1188,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000955416.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625475.1",
"strand": true,
"transcript": "ENST00000955416.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 382,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2974,
"cdna_start": 255,
"cds_end": null,
"cds_length": 1149,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000436005.3",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000414400.3",
"strand": true,
"transcript": "ENST00000436005.3",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 373,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2919,
"cdna_start": 255,
"cds_end": null,
"cds_length": 1122,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000689816.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000508450.1",
"strand": true,
"transcript": "ENST00000689816.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 356,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2903,
"cdna_start": 255,
"cds_end": null,
"cds_length": 1071,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000901529.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000571588.1",
"strand": true,
"transcript": "ENST00000901529.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 344,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2832,
"cdna_start": 255,
"cds_end": null,
"cds_length": 1035,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000688179.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000508635.1",
"strand": true,
"transcript": "ENST00000688179.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 325,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2753,
"cdna_start": 233,
"cds_end": null,
"cds_length": 978,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000687736.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509627.1",
"strand": true,
"transcript": "ENST00000687736.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 258,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2580,
"cdna_start": 233,
"cds_end": null,
"cds_length": 777,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000691220.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509580.1",
"strand": true,
"transcript": "ENST00000691220.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 142,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 631,
"cdna_start": 250,
"cds_end": null,
"cds_length": 429,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001077399.3",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001070867.1",
"strand": true,
"transcript": "NM_001077399.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 356,
"aa_ref": "A",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2900,
"cdna_start": 250,
"cds_end": null,
"cds_length": 1071,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_017003771.2",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016859260.1",
"strand": true,
"transcript": "XM_017003771.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1372,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000469689.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "n.1027C>T",
"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": "ENST00000469689.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1235,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000472650.2",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "n.258C>T",
"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": "ENST00000472650.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3719,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000684905.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "n.244C>T",
"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": "ENST00000684905.1",
"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": 3106,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000690891.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "n.233C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509744.1",
"strand": true,
"transcript": "ENST00000690891.1",
"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": 2203,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000691799.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "n.236C>T",
"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": "ENST00000691799.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1630,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000692260.1",
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"hgvs_c": "n.248C>T",
"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": "ENST00000692260.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1201792156",
"effect": "missense_variant",
"frequency_reference_population": 6.841368e-7,
"gene_hgnc_id": 9153,
"gene_symbol": "PNKD",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84137e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Paroxysmal nonkinesigenic dyskinesia|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.51,
"pos": 218271546,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.658,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_015488.5"
}
]
}