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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: 16-2118216-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2118216&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2118216,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000262304.9",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.776G>A",
"hgvs_p": "p.Cys259Tyr",
"transcript": "NM_001009944.3",
"protein_id": "NP_001009944.3",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 4303,
"cds_start": 776,
"cds_end": null,
"cds_length": 12912,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 14140,
"mane_select": "ENST00000262304.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.776G>A",
"hgvs_p": "p.Cys259Tyr",
"transcript": "ENST00000262304.9",
"protein_id": "ENSP00000262304.4",
"transcript_support_level": 1,
"aa_start": 259,
"aa_end": null,
"aa_length": 4303,
"cds_start": 776,
"cds_end": null,
"cds_length": 12912,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 14140,
"mane_select": "NM_001009944.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.776G>A",
"hgvs_p": "p.Cys259Tyr",
"transcript": "ENST00000423118.5",
"protein_id": "ENSP00000399501.1",
"transcript_support_level": 1,
"aa_start": 259,
"aa_end": null,
"aa_length": 4302,
"cds_start": 776,
"cds_end": null,
"cds_length": 12909,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 14135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.776G>A",
"hgvs_p": "p.Cys259Tyr",
"transcript": "NM_000296.4",
"protein_id": "NP_000287.4",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 4302,
"cds_start": 776,
"cds_end": null,
"cds_length": 12909,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 14137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.776G>A",
"hgvs_p": "p.Cys259Tyr",
"transcript": "XM_047434208.1",
"protein_id": "XP_047290164.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 4348,
"cds_start": 776,
"cds_end": null,
"cds_length": 13047,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 14275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.704G>A",
"hgvs_p": "p.Cys235Tyr",
"transcript": "XM_047434209.1",
"protein_id": "XP_047290165.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 4324,
"cds_start": 704,
"cds_end": null,
"cds_length": 12975,
"cdna_start": 913,
"cdna_end": null,
"cdna_length": 14203,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Cys277Tyr",
"transcript": "XM_011522528.4",
"protein_id": "XP_011520830.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 4321,
"cds_start": 830,
"cds_end": null,
"cds_length": 12966,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 14174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Cys277Tyr",
"transcript": "XM_011522529.3",
"protein_id": "XP_011520831.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 4320,
"cds_start": 830,
"cds_end": null,
"cds_length": 12963,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 14171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.623G>A",
"hgvs_p": "p.Cys208Tyr",
"transcript": "XM_047434210.1",
"protein_id": "XP_047290166.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 4297,
"cds_start": 623,
"cds_end": null,
"cds_length": 12894,
"cdna_start": 1881,
"cdna_end": null,
"cdna_length": 15171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Cys189Tyr",
"transcript": "XM_047434211.1",
"protein_id": "XP_047290167.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 4278,
"cds_start": 566,
"cds_end": null,
"cds_length": 12837,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 14075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.-140G>A",
"hgvs_p": null,
"transcript": "ENST00000488185.2",
"protein_id": "ENSP00000456672.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 244,
"cds_start": -4,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.-92G>A",
"hgvs_p": null,
"transcript": "ENST00000570150.1",
"protein_id": null,
"transcript_support_level": 5,
"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
}
],
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"dbsnp": "rs529066905",
"frequency_reference_population": 0.0002614814,
"hom_count_reference_population": 0,
"allele_count_reference_population": 401,
"gnomad_exomes_af": 0.000263505,
"gnomad_genomes_af": 0.000243114,
"gnomad_exomes_ac": 364,
"gnomad_genomes_ac": 37,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7267004251480103,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.4,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6032,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.183,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000262304.9",
"gene_symbol": "PKD1",
"hgnc_id": 9008,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.776G>A",
"hgvs_p": "p.Cys259Tyr"
}
],
"clinvar_disease": " adult type,PKD1-related disorder,Polycystic kidney disease,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "not provided|PKD1-related disorder|not specified|Polycystic kidney disease, adult type",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}