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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: 16-2090553-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2090553&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2090553,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000262304.9",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12176C>T",
"hgvs_p": "p.Ala4059Val",
"transcript": "NM_001009944.3",
"protein_id": "NP_001009944.3",
"transcript_support_level": null,
"aa_start": 4059,
"aa_end": null,
"aa_length": 4303,
"cds_start": 12176,
"cds_end": null,
"cds_length": 12912,
"cdna_start": 12385,
"cdna_end": null,
"cdna_length": 14140,
"mane_select": "ENST00000262304.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12176C>T",
"hgvs_p": "p.Ala4059Val",
"transcript": "ENST00000262304.9",
"protein_id": "ENSP00000262304.4",
"transcript_support_level": 1,
"aa_start": 4059,
"aa_end": null,
"aa_length": 4303,
"cds_start": 12176,
"cds_end": null,
"cds_length": 12912,
"cdna_start": 12385,
"cdna_end": null,
"cdna_length": 14140,
"mane_select": "NM_001009944.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12173C>T",
"hgvs_p": "p.Ala4058Val",
"transcript": "ENST00000423118.5",
"protein_id": "ENSP00000399501.1",
"transcript_support_level": 1,
"aa_start": 4058,
"aa_end": null,
"aa_length": 4302,
"cds_start": 12173,
"cds_end": null,
"cds_length": 12909,
"cdna_start": 12382,
"cdna_end": null,
"cdna_length": 14135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12173C>T",
"hgvs_p": "p.Ala4058Val",
"transcript": "NM_000296.4",
"protein_id": "NP_000287.4",
"transcript_support_level": null,
"aa_start": 4058,
"aa_end": null,
"aa_length": 4302,
"cds_start": 12173,
"cds_end": null,
"cds_length": 12909,
"cdna_start": 12382,
"cdna_end": null,
"cdna_length": 14137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12311C>T",
"hgvs_p": "p.Ala4104Val",
"transcript": "XM_047434208.1",
"protein_id": "XP_047290164.1",
"transcript_support_level": null,
"aa_start": 4104,
"aa_end": null,
"aa_length": 4348,
"cds_start": 12311,
"cds_end": null,
"cds_length": 13047,
"cdna_start": 12520,
"cdna_end": null,
"cdna_length": 14275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12239C>T",
"hgvs_p": "p.Ala4080Val",
"transcript": "XM_047434209.1",
"protein_id": "XP_047290165.1",
"transcript_support_level": null,
"aa_start": 4080,
"aa_end": null,
"aa_length": 4324,
"cds_start": 12239,
"cds_end": null,
"cds_length": 12975,
"cdna_start": 12448,
"cdna_end": null,
"cdna_length": 14203,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12230C>T",
"hgvs_p": "p.Ala4077Val",
"transcript": "XM_011522528.4",
"protein_id": "XP_011520830.1",
"transcript_support_level": null,
"aa_start": 4077,
"aa_end": null,
"aa_length": 4321,
"cds_start": 12230,
"cds_end": null,
"cds_length": 12966,
"cdna_start": 12419,
"cdna_end": null,
"cdna_length": 14174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12227C>T",
"hgvs_p": "p.Ala4076Val",
"transcript": "XM_011522529.3",
"protein_id": "XP_011520831.1",
"transcript_support_level": null,
"aa_start": 4076,
"aa_end": null,
"aa_length": 4320,
"cds_start": 12227,
"cds_end": null,
"cds_length": 12963,
"cdna_start": 12416,
"cdna_end": null,
"cdna_length": 14171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12158C>T",
"hgvs_p": "p.Ala4053Val",
"transcript": "XM_047434210.1",
"protein_id": "XP_047290166.1",
"transcript_support_level": null,
"aa_start": 4053,
"aa_end": null,
"aa_length": 4297,
"cds_start": 12158,
"cds_end": null,
"cds_length": 12894,
"cdna_start": 13416,
"cdna_end": null,
"cdna_length": 15171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12101C>T",
"hgvs_p": "p.Ala4034Val",
"transcript": "XM_047434211.1",
"protein_id": "XP_047290167.1",
"transcript_support_level": null,
"aa_start": 4034,
"aa_end": null,
"aa_length": 4278,
"cds_start": 12101,
"cds_end": null,
"cds_length": 12837,
"cdna_start": 12320,
"cdna_end": null,
"cdna_length": 14075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.10271C>T",
"hgvs_p": "p.Ala3424Val",
"transcript": "XM_047434212.1",
"protein_id": "XP_047290168.1",
"transcript_support_level": null,
"aa_start": 3424,
"aa_end": null,
"aa_length": 3668,
"cds_start": 10271,
"cds_end": null,
"cds_length": 11007,
"cdna_start": 10372,
"cdna_end": null,
"cdna_length": 12127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.9254C>T",
"hgvs_p": "p.Ala3085Val",
"transcript": "XM_011522537.2",
"protein_id": "XP_011520839.1",
"transcript_support_level": null,
"aa_start": 3085,
"aa_end": null,
"aa_length": 3329,
"cds_start": 9254,
"cds_end": null,
"cds_length": 9990,
"cdna_start": 9343,
"cdna_end": null,
"cdna_length": 11098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.9248C>T",
"hgvs_p": "p.Ala3083Val",
"transcript": "XM_047434213.1",
"protein_id": "XP_047290169.1",
"transcript_support_level": null,
"aa_start": 3083,
"aa_end": null,
"aa_length": 3327,
"cds_start": 9248,
"cds_end": null,
"cds_length": 9984,
"cdna_start": 9337,
"cdna_end": null,
"cdna_length": 11092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.9131C>T",
"hgvs_p": "p.Ala3044Val",
"transcript": "XM_005255370.4",
"protein_id": "XP_005255427.1",
"transcript_support_level": null,
"aa_start": 3044,
"aa_end": null,
"aa_length": 3288,
"cds_start": 9131,
"cds_end": null,
"cds_length": 9867,
"cdna_start": 9303,
"cdna_end": null,
"cdna_length": 11058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.204C>T",
"hgvs_p": null,
"transcript": "ENST00000472577.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_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.*212C>T",
"hgvs_p": null,
"transcript": "ENST00000564313.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"dbsnp": "rs3209986",
"frequency_reference_population": 0.07152525,
"hom_count_reference_population": 4643,
"allele_count_reference_population": 115095,
"gnomad_exomes_af": 0.0730132,
"gnomad_genomes_af": 0.0572913,
"gnomad_exomes_ac": 106370,
"gnomad_genomes_ac": 8725,
"gnomad_exomes_homalt": 4283,
"gnomad_genomes_homalt": 360,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0025211572647094727,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.091,
"revel_prediction": "Benign",
"alphamissense_score": 0.0875,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.236,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000262304.9",
"gene_symbol": "PKD1",
"hgnc_id": 9008,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.12176C>T",
"hgvs_p": "p.Ala4059Val"
}
],
"clinvar_disease": " adult type,Autosomal dominant polycystic kidney disease,Polycystic kidney disease,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:6",
"phenotype_combined": "not specified|Autosomal dominant polycystic kidney disease|Polycystic kidney disease|Polycystic kidney disease, adult type|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}