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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: 17-80111023-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=80111023&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 80111023,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000302262.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "NM_000152.5",
"protein_id": "NP_000143.2",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1976,
"cdna_end": null,
"cdna_length": 3751,
"mane_select": "ENST00000302262.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "ENST00000302262.8",
"protein_id": "ENSP00000305692.3",
"transcript_support_level": 1,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1976,
"cdna_end": null,
"cdna_length": 3751,
"mane_select": "NM_000152.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "ENST00000390015.7",
"protein_id": "ENSP00000374665.3",
"transcript_support_level": 1,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1778,
"cdna_end": null,
"cdna_length": 3549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "NM_001079803.3",
"protein_id": "NP_001073271.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1791,
"cdna_end": null,
"cdna_length": 3566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "NM_001079804.3",
"protein_id": "NP_001073272.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1711,
"cdna_end": null,
"cdna_length": 3486,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "NM_001406741.1",
"protein_id": "NP_001393670.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1886,
"cdna_end": null,
"cdna_length": 3661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "NM_001406742.1",
"protein_id": "NP_001393671.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1826,
"cdna_end": null,
"cdna_length": 3601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "ENST00000570803.6",
"protein_id": "ENSP00000460543.2",
"transcript_support_level": 5,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1759,
"cdna_end": null,
"cdna_length": 3522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "ENST00000577106.6",
"protein_id": "ENSP00000458306.2",
"transcript_support_level": 3,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1831,
"cdna_end": null,
"cdna_length": 3594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "ENST00000714057.1",
"protein_id": "ENSP00000519347.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1928,
"cdna_end": null,
"cdna_length": 3537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "ENST00000714058.1",
"protein_id": "ENSP00000519348.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 1810,
"cdna_end": null,
"cdna_length": 3571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "ENST00000714055.1",
"protein_id": "ENSP00000519345.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 922,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 1976,
"cdna_end": null,
"cdna_length": 3657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.833C>T",
"hgvs_p": "p.Pro278Leu",
"transcript": "ENST00000714054.1",
"protein_id": "ENSP00000519344.1",
"transcript_support_level": null,
"aa_start": 278,
"aa_end": null,
"aa_length": 685,
"cds_start": 833,
"cds_end": null,
"cds_length": 2058,
"cdna_start": 1138,
"cdna_end": null,
"cdna_length": 2455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.713C>T",
"hgvs_p": "p.Pro238Leu",
"transcript": "ENST00000714062.1",
"protein_id": "ENSP00000519352.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 645,
"cds_start": 713,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 2771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu",
"transcript": "XM_047435719.1",
"protein_id": "XP_047291675.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 952,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 2011,
"cdna_end": null,
"cdna_length": 3786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "n.1634C>T",
"hgvs_p": null,
"transcript": "ENST00000572080.2",
"protein_id": "ENSP00000459972.2",
"transcript_support_level": 3,
"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": 3594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "n.1634C>T",
"hgvs_p": null,
"transcript": "ENST00000714056.1",
"protein_id": "ENSP00000519346.1",
"transcript_support_level": null,
"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": 3666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "n.*973C>T",
"hgvs_p": null,
"transcript": "ENST00000714061.1",
"protein_id": "ENSP00000519351.1",
"transcript_support_level": null,
"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": 3826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"hgvs_c": "n.*973C>T",
"hgvs_p": null,
"transcript": "ENST00000714061.1",
"protein_id": "ENSP00000519351.1",
"transcript_support_level": null,
"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": 3826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GAA",
"gene_hgnc_id": 4065,
"dbsnp": "rs121907942",
"frequency_reference_population": 0.000009915827,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000889569,
"gnomad_genomes_af": 0.0000197109,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.957087516784668,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9520000219345093,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.838,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7676,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.43,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.829,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999638193343409,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000302262.8",
"gene_symbol": "GAA",
"hgnc_id": 4065,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1634C>T",
"hgvs_p": "p.Pro545Leu"
}
],
"clinvar_disease": " ADULT FORM, type II,GLYCOGEN STORAGE DISEASE II,Glycogen storage disease,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5",
"phenotype_combined": "GLYCOGEN STORAGE DISEASE II, ADULT FORM|not provided|Glycogen storage disease, type II",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}