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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: 16-2089874-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2089874&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2089874,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000262304.9",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12765C>T",
"hgvs_p": "p.Pro4255Pro",
"transcript": "NM_001009944.3",
"protein_id": "NP_001009944.3",
"transcript_support_level": null,
"aa_start": 4255,
"aa_end": null,
"aa_length": 4303,
"cds_start": 12765,
"cds_end": null,
"cds_length": 12912,
"cdna_start": 12974,
"cdna_end": null,
"cdna_length": 14140,
"mane_select": "ENST00000262304.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12765C>T",
"hgvs_p": "p.Pro4255Pro",
"transcript": "ENST00000262304.9",
"protein_id": "ENSP00000262304.4",
"transcript_support_level": 1,
"aa_start": 4255,
"aa_end": null,
"aa_length": 4303,
"cds_start": 12765,
"cds_end": null,
"cds_length": 12912,
"cdna_start": 12974,
"cdna_end": null,
"cdna_length": 14140,
"mane_select": "NM_001009944.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12762C>T",
"hgvs_p": "p.Pro4254Pro",
"transcript": "ENST00000423118.5",
"protein_id": "ENSP00000399501.1",
"transcript_support_level": 1,
"aa_start": 4254,
"aa_end": null,
"aa_length": 4302,
"cds_start": 12762,
"cds_end": null,
"cds_length": 12909,
"cdna_start": 12971,
"cdna_end": null,
"cdna_length": 14135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12762C>T",
"hgvs_p": "p.Pro4254Pro",
"transcript": "NM_000296.4",
"protein_id": "NP_000287.4",
"transcript_support_level": null,
"aa_start": 4254,
"aa_end": null,
"aa_length": 4302,
"cds_start": 12762,
"cds_end": null,
"cds_length": 12909,
"cdna_start": 12971,
"cdna_end": null,
"cdna_length": 14137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12900C>T",
"hgvs_p": "p.Pro4300Pro",
"transcript": "XM_047434208.1",
"protein_id": "XP_047290164.1",
"transcript_support_level": null,
"aa_start": 4300,
"aa_end": null,
"aa_length": 4348,
"cds_start": 12900,
"cds_end": null,
"cds_length": 13047,
"cdna_start": 13109,
"cdna_end": null,
"cdna_length": 14275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12828C>T",
"hgvs_p": "p.Pro4276Pro",
"transcript": "XM_047434209.1",
"protein_id": "XP_047290165.1",
"transcript_support_level": null,
"aa_start": 4276,
"aa_end": null,
"aa_length": 4324,
"cds_start": 12828,
"cds_end": null,
"cds_length": 12975,
"cdna_start": 13037,
"cdna_end": null,
"cdna_length": 14203,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12819C>T",
"hgvs_p": "p.Pro4273Pro",
"transcript": "XM_011522528.4",
"protein_id": "XP_011520830.1",
"transcript_support_level": null,
"aa_start": 4273,
"aa_end": null,
"aa_length": 4321,
"cds_start": 12819,
"cds_end": null,
"cds_length": 12966,
"cdna_start": 13008,
"cdna_end": null,
"cdna_length": 14174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12816C>T",
"hgvs_p": "p.Pro4272Pro",
"transcript": "XM_011522529.3",
"protein_id": "XP_011520831.1",
"transcript_support_level": null,
"aa_start": 4272,
"aa_end": null,
"aa_length": 4320,
"cds_start": 12816,
"cds_end": null,
"cds_length": 12963,
"cdna_start": 13005,
"cdna_end": null,
"cdna_length": 14171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12747C>T",
"hgvs_p": "p.Pro4249Pro",
"transcript": "XM_047434210.1",
"protein_id": "XP_047290166.1",
"transcript_support_level": null,
"aa_start": 4249,
"aa_end": null,
"aa_length": 4297,
"cds_start": 12747,
"cds_end": null,
"cds_length": 12894,
"cdna_start": 14005,
"cdna_end": null,
"cdna_length": 15171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.12690C>T",
"hgvs_p": "p.Pro4230Pro",
"transcript": "XM_047434211.1",
"protein_id": "XP_047290167.1",
"transcript_support_level": null,
"aa_start": 4230,
"aa_end": null,
"aa_length": 4278,
"cds_start": 12690,
"cds_end": null,
"cds_length": 12837,
"cdna_start": 12909,
"cdna_end": null,
"cdna_length": 14075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.10860C>T",
"hgvs_p": "p.Pro3620Pro",
"transcript": "XM_047434212.1",
"protein_id": "XP_047290168.1",
"transcript_support_level": null,
"aa_start": 3620,
"aa_end": null,
"aa_length": 3668,
"cds_start": 10860,
"cds_end": null,
"cds_length": 11007,
"cdna_start": 10961,
"cdna_end": null,
"cdna_length": 12127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.9843C>T",
"hgvs_p": "p.Pro3281Pro",
"transcript": "XM_011522537.2",
"protein_id": "XP_011520839.1",
"transcript_support_level": null,
"aa_start": 3281,
"aa_end": null,
"aa_length": 3329,
"cds_start": 9843,
"cds_end": null,
"cds_length": 9990,
"cdna_start": 9932,
"cdna_end": null,
"cdna_length": 11098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.9837C>T",
"hgvs_p": "p.Pro3279Pro",
"transcript": "XM_047434213.1",
"protein_id": "XP_047290169.1",
"transcript_support_level": null,
"aa_start": 3279,
"aa_end": null,
"aa_length": 3327,
"cds_start": 9837,
"cds_end": null,
"cds_length": 9984,
"cdna_start": 9926,
"cdna_end": null,
"cdna_length": 11092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "c.9720C>T",
"hgvs_p": "p.Pro3240Pro",
"transcript": "XM_005255370.4",
"protein_id": "XP_005255427.1",
"transcript_support_level": null,
"aa_start": 3240,
"aa_end": null,
"aa_length": 3288,
"cds_start": 9720,
"cds_end": null,
"cds_length": 9867,
"cdna_start": 9892,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"hgvs_c": "n.793C>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
}
],
"gene_symbol": "PKD1",
"gene_hgnc_id": 9008,
"dbsnp": "rs62038811",
"frequency_reference_population": 0.0066232323,
"hom_count_reference_population": 49,
"allele_count_reference_population": 10662,
"gnomad_exomes_af": 0.00687029,
"gnomad_genomes_af": 0.00425982,
"gnomad_exomes_ac": 10013,
"gnomad_genomes_ac": 649,
"gnomad_exomes_homalt": 48,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.62,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000262304.9",
"gene_symbol": "PKD1",
"hgnc_id": 9008,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.12765C>T",
"hgvs_p": "p.Pro4255Pro"
}
],
"clinvar_disease": " adult type,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:4 B:2",
"phenotype_combined": "Polycystic kidney disease|Polycystic kidney disease, adult type|not provided|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}