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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: 16-2091144-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2091144&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PKD1",
"hgnc_id": 9008,
"hgvs_c": "c.11743G>A",
"hgvs_p": "p.Ala3915Thr",
"inheritance_mode": "AD,AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_001009944.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2",
"acmg_score": 4,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.0888,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.47,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5433796644210815,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4303,
"aa_ref": "A",
"aa_start": 3915,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14140,
"cdna_start": 11952,
"cds_end": null,
"cds_length": 12912,
"cds_start": 11743,
"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.11743G>A",
"hgvs_p": "p.Ala3915Thr",
"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": "T",
"aa_end": null,
"aa_length": 4303,
"aa_ref": "A",
"aa_start": 3915,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 14140,
"cdna_start": 11952,
"cds_end": null,
"cds_length": 12912,
"cds_start": 11743,
"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.11743G>A",
"hgvs_p": "p.Ala3915Thr",
"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": "T",
"aa_end": null,
"aa_length": 4302,
"aa_ref": "A",
"aa_start": 3914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14135,
"cdna_start": 11949,
"cds_end": null,
"cds_length": 12909,
"cds_start": 11740,
"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.11740G>A",
"hgvs_p": "p.Ala3914Thr",
"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": "T",
"aa_end": null,
"aa_length": 4302,
"aa_ref": "A",
"aa_start": 3914,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14137,
"cdna_start": 11949,
"cds_end": null,
"cds_length": 12909,
"cds_start": 11740,
"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.11740G>A",
"hgvs_p": "p.Ala3914Thr",
"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": "T",
"aa_end": null,
"aa_length": 4348,
"aa_ref": "A",
"aa_start": 3960,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14275,
"cdna_start": 12087,
"cds_end": null,
"cds_length": 13047,
"cds_start": 11878,
"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.11878G>A",
"hgvs_p": "p.Ala3960Thr",
"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": "T",
"aa_end": null,
"aa_length": 4324,
"aa_ref": "A",
"aa_start": 3936,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14203,
"cdna_start": 12015,
"cds_end": null,
"cds_length": 12975,
"cds_start": 11806,
"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.11806G>A",
"hgvs_p": "p.Ala3936Thr",
"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": "T",
"aa_end": null,
"aa_length": 4321,
"aa_ref": "A",
"aa_start": 3933,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14174,
"cdna_start": 11986,
"cds_end": null,
"cds_length": 12966,
"cds_start": 11797,
"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.11797G>A",
"hgvs_p": "p.Ala3933Thr",
"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": "T",
"aa_end": null,
"aa_length": 4320,
"aa_ref": "A",
"aa_start": 3932,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14171,
"cdna_start": 11983,
"cds_end": null,
"cds_length": 12963,
"cds_start": 11794,
"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.11794G>A",
"hgvs_p": "p.Ala3932Thr",
"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": "T",
"aa_end": null,
"aa_length": 4297,
"aa_ref": "A",
"aa_start": 3909,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15171,
"cdna_start": 12983,
"cds_end": null,
"cds_length": 12894,
"cds_start": 11725,
"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.11725G>A",
"hgvs_p": "p.Ala3909Thr",
"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": "T",
"aa_end": null,
"aa_length": 4278,
"aa_ref": "A",
"aa_start": 3890,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14075,
"cdna_start": 11887,
"cds_end": null,
"cds_length": 12837,
"cds_start": 11668,
"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.11668G>A",
"hgvs_p": "p.Ala3890Thr",
"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": "T",
"aa_end": null,
"aa_length": 3668,
"aa_ref": "A",
"aa_start": 3280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12127,
"cdna_start": 9939,
"cds_end": null,
"cds_length": 11007,
"cds_start": 9838,
"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.9838G>A",
"hgvs_p": "p.Ala3280Thr",
"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": "T",
"aa_end": null,
"aa_length": 3329,
"aa_ref": "A",
"aa_start": 2941,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11098,
"cdna_start": 8910,
"cds_end": null,
"cds_length": 9990,
"cds_start": 8821,
"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.8821G>A",
"hgvs_p": "p.Ala2941Thr",
"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": "T",
"aa_end": null,
"aa_length": 3327,
"aa_ref": "A",
"aa_start": 2939,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11092,
"cdna_start": 8904,
"cds_end": null,
"cds_length": 9984,
"cds_start": 8815,
"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.8815G>A",
"hgvs_p": "p.Ala2939Thr",
"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": "T",
"aa_end": null,
"aa_length": 3288,
"aa_ref": "A",
"aa_start": 2900,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11058,
"cdna_start": 8870,
"cds_end": null,
"cds_length": 9867,
"cds_start": 8698,
"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.8698G>A",
"hgvs_p": "p.Ala2900Thr",
"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.*2936G>A",
"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.*267G>A",
"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.264G>A",
"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.*2936G>A",
"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.*267G>A",
"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
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1555445237",
"effect": "missense_variant",
"frequency_reference_population": 7.5382945e-7,
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 7.53829e-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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.116,
"pos": 2091144,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.144,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_001009944.3"
}
]
}