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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: 16-2090688-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2090688&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "PKD1",
"hgnc_id": 9008,
"hgvs_c": "c.12124C>T",
"hgvs_p": "p.Gln4042*",
"inheritance_mode": "AD,AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_001009944.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.52,
"chr": "16",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " adult type,Polycystic kidney disease,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.5199999809265137,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4303,
"aa_ref": "Q",
"aa_start": 4042,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14140,
"cdna_start": 12333,
"cds_end": null,
"cds_length": 12912,
"cds_start": 12124,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "NM_001009944.3",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12124C>T",
"hgvs_p": "p.Gln4042*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262304.9",
"protein_coding": true,
"protein_id": "NP_001009944.3",
"strand": false,
"transcript": "NM_001009944.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4303,
"aa_ref": "Q",
"aa_start": 4042,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 14140,
"cdna_start": 12333,
"cds_end": null,
"cds_length": 12912,
"cds_start": 12124,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "ENST00000262304.9",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12124C>T",
"hgvs_p": "p.Gln4042*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001009944.3",
"protein_coding": true,
"protein_id": "ENSP00000262304.4",
"strand": false,
"transcript": "ENST00000262304.9",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4302,
"aa_ref": "Q",
"aa_start": 4041,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14135,
"cdna_start": 12330,
"cds_end": null,
"cds_length": 12909,
"cds_start": 12121,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "ENST00000423118.5",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12121C>T",
"hgvs_p": "p.Gln4041*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000399501.1",
"strand": false,
"transcript": "ENST00000423118.5",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4302,
"aa_ref": "Q",
"aa_start": 4041,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14137,
"cdna_start": 12330,
"cds_end": null,
"cds_length": 12909,
"cds_start": 12121,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "NM_000296.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12121C>T",
"hgvs_p": "p.Gln4041*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_000287.4",
"strand": false,
"transcript": "NM_000296.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4348,
"aa_ref": "Q",
"aa_start": 4087,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14275,
"cdna_start": 12468,
"cds_end": null,
"cds_length": 13047,
"cds_start": 12259,
"consequences": [
"stop_gained"
],
"exon_count": 48,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_047434208.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12259C>T",
"hgvs_p": "p.Gln4087*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290164.1",
"strand": false,
"transcript": "XM_047434208.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4324,
"aa_ref": "Q",
"aa_start": 4063,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14203,
"cdna_start": 12396,
"cds_end": null,
"cds_length": 12975,
"cds_start": 12187,
"consequences": [
"stop_gained"
],
"exon_count": 47,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_047434209.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12187C>T",
"hgvs_p": "p.Gln4063*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290165.1",
"strand": false,
"transcript": "XM_047434209.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4321,
"aa_ref": "Q",
"aa_start": 4060,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14174,
"cdna_start": 12367,
"cds_end": null,
"cds_length": 12966,
"cds_start": 12178,
"consequences": [
"stop_gained"
],
"exon_count": 47,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_011522528.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12178C>T",
"hgvs_p": "p.Gln4060*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011520830.1",
"strand": false,
"transcript": "XM_011522528.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4320,
"aa_ref": "Q",
"aa_start": 4059,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14171,
"cdna_start": 12364,
"cds_end": null,
"cds_length": 12963,
"cds_start": 12175,
"consequences": [
"stop_gained"
],
"exon_count": 47,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_011522529.3",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12175C>T",
"hgvs_p": "p.Gln4059*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011520831.1",
"strand": false,
"transcript": "XM_011522529.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4297,
"aa_ref": "Q",
"aa_start": 4036,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15171,
"cdna_start": 13364,
"cds_end": null,
"cds_length": 12894,
"cds_start": 12106,
"consequences": [
"stop_gained"
],
"exon_count": 48,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_047434210.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12106C>T",
"hgvs_p": "p.Gln4036*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290166.1",
"strand": false,
"transcript": "XM_047434210.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 4278,
"aa_ref": "Q",
"aa_start": 4017,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14075,
"cdna_start": 12268,
"cds_end": null,
"cds_length": 12837,
"cds_start": 12049,
"consequences": [
"stop_gained"
],
"exon_count": 48,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_047434211.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12049C>T",
"hgvs_p": "p.Gln4017*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290167.1",
"strand": false,
"transcript": "XM_047434211.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 3668,
"aa_ref": "Q",
"aa_start": 3407,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12127,
"cdna_start": 10320,
"cds_end": null,
"cds_length": 11007,
"cds_start": 10219,
"consequences": [
"stop_gained"
],
"exon_count": 39,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "XM_047434212.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.10219C>T",
"hgvs_p": "p.Gln3407*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290168.1",
"strand": false,
"transcript": "XM_047434212.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 3329,
"aa_ref": "Q",
"aa_start": 3068,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11098,
"cdna_start": 9291,
"cds_end": null,
"cds_length": 9990,
"cds_start": 9202,
"consequences": [
"stop_gained"
],
"exon_count": 36,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_011522537.2",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.9202C>T",
"hgvs_p": "p.Gln3068*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011520839.1",
"strand": false,
"transcript": "XM_011522537.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 3327,
"aa_ref": "Q",
"aa_start": 3066,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11092,
"cdna_start": 9285,
"cds_end": null,
"cds_length": 9984,
"cds_start": 9196,
"consequences": [
"stop_gained"
],
"exon_count": 36,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_047434213.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.9196C>T",
"hgvs_p": "p.Gln3066*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290169.1",
"strand": false,
"transcript": "XM_047434213.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 3288,
"aa_ref": "Q",
"aa_start": 3027,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11058,
"cdna_start": 9251,
"cds_end": null,
"cds_length": 9867,
"cds_start": 9079,
"consequences": [
"stop_gained"
],
"exon_count": 35,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "XM_005255370.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.9079C>T",
"hgvs_p": "p.Gln3027*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005255427.1",
"strand": false,
"transcript": "XM_005255370.4",
"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": 1140,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000472577.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.152C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000472577.1",
"transcript_support_level": 2
},
{
"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": 665,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000561668.5",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.*723C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000461391.1",
"strand": true,
"transcript": "ENST00000561668.5",
"transcript_support_level": 3
},
{
"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": 568,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000564313.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.*77C>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": "ENST00000564313.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199476094",
"effect": "stop_gained",
"frequency_reference_population": 0.0000013698743,
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136987,
"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": "Pathogenic",
"phenotype_combined": "Polycystic kidney disease, adult type|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.328,
"pos": 2090688,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001009944.3"
}
]
}