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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: 16-2091012-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2091012&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PKD1",
"hgnc_id": 9008,
"hgvs_c": "c.11875G>C",
"hgvs_p": "p.Ala3959Pro",
"inheritance_mode": "AD,AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_001009944.3",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate",
"acmg_score": 6,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.8779,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.17,
"chr": "16",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " adult type,Polycystic kidney disease,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8692066073417664,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 4303,
"aa_ref": "A",
"aa_start": 3959,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14140,
"cdna_start": 12084,
"cds_end": null,
"cds_length": 12912,
"cds_start": 11875,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 43,
"exon_rank_end": null,
"feature": "NM_001009944.3",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11875G>C",
"hgvs_p": "p.Ala3959Pro",
"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": "P",
"aa_end": null,
"aa_length": 4303,
"aa_ref": "A",
"aa_start": 3959,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 14140,
"cdna_start": 12084,
"cds_end": null,
"cds_length": 12912,
"cds_start": 11875,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 43,
"exon_rank_end": null,
"feature": "ENST00000262304.9",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11875G>C",
"hgvs_p": "p.Ala3959Pro",
"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": "P",
"aa_end": null,
"aa_length": 4302,
"aa_ref": "A",
"aa_start": 3958,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14135,
"cdna_start": 12081,
"cds_end": null,
"cds_length": 12909,
"cds_start": 11872,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 43,
"exon_rank_end": null,
"feature": "ENST00000423118.5",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11872G>C",
"hgvs_p": "p.Ala3958Pro",
"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": "P",
"aa_end": null,
"aa_length": 4302,
"aa_ref": "A",
"aa_start": 3958,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14137,
"cdna_start": 12081,
"cds_end": null,
"cds_length": 12909,
"cds_start": 11872,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 43,
"exon_rank_end": null,
"feature": "NM_000296.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11872G>C",
"hgvs_p": "p.Ala3958Pro",
"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": "P",
"aa_end": null,
"aa_length": 4348,
"aa_ref": "A",
"aa_start": 4004,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14275,
"cdna_start": 12219,
"cds_end": null,
"cds_length": 13047,
"cds_start": 12010,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_047434208.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12010G>C",
"hgvs_p": "p.Ala4004Pro",
"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": "P",
"aa_end": null,
"aa_length": 4324,
"aa_ref": "A",
"aa_start": 3980,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14203,
"cdna_start": 12147,
"cds_end": null,
"cds_length": 12975,
"cds_start": 11938,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "XM_047434209.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11938G>C",
"hgvs_p": "p.Ala3980Pro",
"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": "P",
"aa_end": null,
"aa_length": 4321,
"aa_ref": "A",
"aa_start": 3977,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14174,
"cdna_start": 12118,
"cds_end": null,
"cds_length": 12966,
"cds_start": 11929,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "XM_011522528.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11929G>C",
"hgvs_p": "p.Ala3977Pro",
"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": "P",
"aa_end": null,
"aa_length": 4320,
"aa_ref": "A",
"aa_start": 3976,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14171,
"cdna_start": 12115,
"cds_end": null,
"cds_length": 12963,
"cds_start": 11926,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "XM_011522529.3",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11926G>C",
"hgvs_p": "p.Ala3976Pro",
"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": "P",
"aa_end": null,
"aa_length": 4297,
"aa_ref": "A",
"aa_start": 3953,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15171,
"cdna_start": 13115,
"cds_end": null,
"cds_length": 12894,
"cds_start": 11857,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_047434210.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11857G>C",
"hgvs_p": "p.Ala3953Pro",
"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": "P",
"aa_end": null,
"aa_length": 4278,
"aa_ref": "A",
"aa_start": 3934,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14075,
"cdna_start": 12019,
"cds_end": null,
"cds_length": 12837,
"cds_start": 11800,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_047434211.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.11800G>C",
"hgvs_p": "p.Ala3934Pro",
"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": "P",
"aa_end": null,
"aa_length": 3668,
"aa_ref": "A",
"aa_start": 3324,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12127,
"cdna_start": 10071,
"cds_end": null,
"cds_length": 11007,
"cds_start": 9970,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "XM_047434212.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.9970G>C",
"hgvs_p": "p.Ala3324Pro",
"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": "P",
"aa_end": null,
"aa_length": 3329,
"aa_ref": "A",
"aa_start": 2985,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11098,
"cdna_start": 9042,
"cds_end": null,
"cds_length": 9990,
"cds_start": 8953,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "XM_011522537.2",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.8953G>C",
"hgvs_p": "p.Ala2985Pro",
"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": "P",
"aa_end": null,
"aa_length": 3327,
"aa_ref": "A",
"aa_start": 2983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11092,
"cdna_start": 9036,
"cds_end": null,
"cds_length": 9984,
"cds_start": 8947,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "XM_047434213.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.8947G>C",
"hgvs_p": "p.Ala2983Pro",
"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": "P",
"aa_end": null,
"aa_length": 3288,
"aa_ref": "A",
"aa_start": 2944,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11058,
"cdna_start": 9002,
"cds_end": null,
"cds_length": 9867,
"cds_start": 8830,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "XM_005255370.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.8830G>C",
"hgvs_p": "p.Ala2944Pro",
"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": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6464,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 30,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000487932.5",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.*3068G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000457132.1",
"strand": false,
"transcript": "ENST00000487932.5",
"transcript_support_level": 5
},
{
"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": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000561668.5",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.*399G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000461391.1",
"strand": false,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000564313.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.396G>C",
"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": "ENST00000564313.1",
"transcript_support_level": 4
},
{
"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": 6464,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 30,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000487932.5",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.*3068G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000457132.1",
"strand": false,
"transcript": "ENST00000487932.5",
"transcript_support_level": 5
},
{
"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": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000561668.5",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.*399G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000461391.1",
"strand": false,
"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": 1140,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000472577.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.-173G>C",
"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": "ENST00000472577.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs756245085",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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": "Polycystic kidney disease, adult type|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.512,
"pos": 2091012,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.533,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_001009944.3"
}
]
}