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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: 16-2090322-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2090322&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PKD1",
"hgnc_id": 9008,
"hgvs_c": "c.12407G>A",
"hgvs_p": "p.Arg4136Lys",
"inheritance_mode": "AD,AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_001009944.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "MIR1225",
"hgnc_id": 33931,
"hgvs_c": "n.-38G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "NR_030646.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM5",
"acmg_score": 4,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.6962,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.15,
"chr": "16",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.68709397315979,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 4303,
"aa_ref": "R",
"aa_start": 4136,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14140,
"cdna_start": 12616,
"cds_end": null,
"cds_length": 12912,
"cds_start": 12407,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "NM_001009944.3",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12407G>A",
"hgvs_p": "p.Arg4136Lys",
"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": "K",
"aa_end": null,
"aa_length": 4303,
"aa_ref": "R",
"aa_start": 4136,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 14140,
"cdna_start": 12616,
"cds_end": null,
"cds_length": 12912,
"cds_start": 12407,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000262304.9",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12407G>A",
"hgvs_p": "p.Arg4136Lys",
"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": "K",
"aa_end": null,
"aa_length": 4302,
"aa_ref": "R",
"aa_start": 4135,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14135,
"cdna_start": 12613,
"cds_end": null,
"cds_length": 12909,
"cds_start": 12404,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "ENST00000423118.5",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12404G>A",
"hgvs_p": "p.Arg4135Lys",
"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": "K",
"aa_end": null,
"aa_length": 4302,
"aa_ref": "R",
"aa_start": 4135,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14137,
"cdna_start": 12613,
"cds_end": null,
"cds_length": 12909,
"cds_start": 12404,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "NM_000296.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12404G>A",
"hgvs_p": "p.Arg4135Lys",
"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": "K",
"aa_end": null,
"aa_length": 4348,
"aa_ref": "R",
"aa_start": 4181,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14275,
"cdna_start": 12751,
"cds_end": null,
"cds_length": 13047,
"cds_start": 12542,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "XM_047434208.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12542G>A",
"hgvs_p": "p.Arg4181Lys",
"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": "K",
"aa_end": null,
"aa_length": 4324,
"aa_ref": "R",
"aa_start": 4157,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14203,
"cdna_start": 12679,
"cds_end": null,
"cds_length": 12975,
"cds_start": 12470,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_047434209.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12470G>A",
"hgvs_p": "p.Arg4157Lys",
"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": "K",
"aa_end": null,
"aa_length": 4321,
"aa_ref": "R",
"aa_start": 4154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14174,
"cdna_start": 12650,
"cds_end": null,
"cds_length": 12966,
"cds_start": 12461,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_011522528.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12461G>A",
"hgvs_p": "p.Arg4154Lys",
"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": "K",
"aa_end": null,
"aa_length": 4320,
"aa_ref": "R",
"aa_start": 4153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14171,
"cdna_start": 12647,
"cds_end": null,
"cds_length": 12963,
"cds_start": 12458,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_011522529.3",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12458G>A",
"hgvs_p": "p.Arg4153Lys",
"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": "K",
"aa_end": null,
"aa_length": 4297,
"aa_ref": "R",
"aa_start": 4130,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15171,
"cdna_start": 13647,
"cds_end": null,
"cds_length": 12894,
"cds_start": 12389,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "XM_047434210.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12389G>A",
"hgvs_p": "p.Arg4130Lys",
"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": "K",
"aa_end": null,
"aa_length": 4278,
"aa_ref": "R",
"aa_start": 4111,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14075,
"cdna_start": 12551,
"cds_end": null,
"cds_length": 12837,
"cds_start": 12332,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "XM_047434211.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.12332G>A",
"hgvs_p": "p.Arg4111Lys",
"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": "K",
"aa_end": null,
"aa_length": 3668,
"aa_ref": "R",
"aa_start": 3501,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12127,
"cdna_start": 10603,
"cds_end": null,
"cds_length": 11007,
"cds_start": 10502,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 38,
"exon_rank_end": null,
"feature": "XM_047434212.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.10502G>A",
"hgvs_p": "p.Arg3501Lys",
"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": "K",
"aa_end": null,
"aa_length": 3329,
"aa_ref": "R",
"aa_start": 3162,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11098,
"cdna_start": 9574,
"cds_end": null,
"cds_length": 9990,
"cds_start": 9485,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_011522537.2",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.9485G>A",
"hgvs_p": "p.Arg3162Lys",
"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": "K",
"aa_end": null,
"aa_length": 3327,
"aa_ref": "R",
"aa_start": 3160,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11092,
"cdna_start": 9568,
"cds_end": null,
"cds_length": 9984,
"cds_start": 9479,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_047434213.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.9479G>A",
"hgvs_p": "p.Arg3160Lys",
"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": "K",
"aa_end": null,
"aa_length": 3288,
"aa_ref": "R",
"aa_start": 3121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11058,
"cdna_start": 9534,
"cds_end": null,
"cds_length": 9867,
"cds_start": 9362,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_005255370.4",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "c.9362G>A",
"hgvs_p": "p.Arg3121Lys",
"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": 2,
"exon_rank_end": null,
"feature": "ENST00000472577.1",
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"hgvs_c": "n.435G>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": "ENST00000472577.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "miRNA",
"canonical": false,
"cdna_end": null,
"cdna_length": 90,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000408729.1",
"gene_hgnc_id": 33931,
"gene_symbol": "MIR1225",
"hgvs_c": "n.-38G>A",
"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": "ENST00000408729.1",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 90,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_030646.1",
"gene_hgnc_id": 33931,
"gene_symbol": "MIR1225",
"hgvs_c": "n.-38G>A",
"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": "NR_030646.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "miRNA",
"canonical": null,
"cdna_end": null,
"cdna_length": 22,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "unassigned_transcript_2769",
"gene_hgnc_id": 33931,
"gene_symbol": "MIR1225",
"hgvs_c": "n.-106G>A",
"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": "unassigned_transcript_2769",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "miRNA",
"canonical": null,
"cdna_end": null,
"cdna_length": 22,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "unassigned_transcript_2770",
"gene_hgnc_id": 33931,
"gene_symbol": "MIR1225",
"hgvs_c": "n.-38G>A",
"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": "unassigned_transcript_2770",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs768391524",
"effect": "missense_variant",
"frequency_reference_population": 6.8512765e-7,
"gene_hgnc_id": 9008,
"gene_symbol": "PKD1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.85128e-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": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.246,
"pos": 2090322,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.388,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05000000074505806,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.05,
"transcript": "NM_001009944.3"
}
]
}