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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: 9-12704564-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=12704564&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "TYRP1",
"hgnc_id": 12450,
"hgvs_c": "c.1120C>T",
"hgvs_p": "p.Arg374*",
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000550.3",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "LURAP1L-AS1",
"hgnc_id": 49761,
"hgvs_c": "n.386G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 14,
"score": 14,
"transcript": "ENST00000803543.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 78,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.55,
"chr": "9",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "MELANESIAN BLOND HAIR,Oculocutaneous albinism type 3,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.550000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 537,
"aa_ref": "R",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2896,
"cdna_start": 1299,
"cds_end": null,
"cds_length": 1614,
"cds_start": 1120,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_000550.3",
"gene_hgnc_id": 12450,
"gene_symbol": "TYRP1",
"hgvs_c": "c.1120C>T",
"hgvs_p": "p.Arg374*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000388918.10",
"protein_coding": true,
"protein_id": "NP_000541.1",
"strand": true,
"transcript": "NM_000550.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 537,
"aa_ref": "R",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2896,
"cdna_start": 1299,
"cds_end": null,
"cds_length": 1614,
"cds_start": 1120,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000388918.10",
"gene_hgnc_id": 12450,
"gene_symbol": "TYRP1",
"hgvs_c": "c.1120C>T",
"hgvs_p": "p.Arg374*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000550.3",
"protein_coding": true,
"protein_id": "ENSP00000373570.4",
"strand": true,
"transcript": "ENST00000388918.10",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 247,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 872,
"cdna_start": 325,
"cds_end": null,
"cds_length": 744,
"cds_start": 250,
"consequences": [
"stop_gained"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000381136.2",
"gene_hgnc_id": 12450,
"gene_symbol": "TYRP1",
"hgvs_c": "c.250C>T",
"hgvs_p": "p.Arg84*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000370528.2",
"strand": true,
"transcript": "ENST00000381136.2",
"transcript_support_level": 2
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 315,
"aa_ref": "F",
"aa_start": 305,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1235,
"cdna_start": 1094,
"cds_end": null,
"cds_length": 948,
"cds_start": 915,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047423841.1",
"gene_hgnc_id": 12450,
"gene_symbol": "TYRP1",
"hgvs_c": "c.915C>T",
"hgvs_p": "p.Phe305Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279797.1",
"strand": true,
"transcript": "XM_047423841.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 789,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000381142.3",
"gene_hgnc_id": 12450,
"gene_symbol": "TYRP1",
"hgvs_c": "n.357C>T",
"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": "ENST00000381142.3",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 837,
"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": "ENST00000803543.1",
"gene_hgnc_id": 49761,
"gene_symbol": "LURAP1L-AS1",
"hgvs_c": "n.386G>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": "ENST00000803543.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1028,
"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": "ENST00000803545.1",
"gene_hgnc_id": 49761,
"gene_symbol": "LURAP1L-AS1",
"hgvs_c": "n.344G>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": "ENST00000803545.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 799,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000417638.1",
"gene_hgnc_id": 49761,
"gene_symbol": "LURAP1L-AS1",
"hgvs_c": "n.273-3938G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000417638.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 994,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650458.1",
"gene_hgnc_id": 49761,
"gene_symbol": "LURAP1L-AS1",
"hgvs_c": "n.193-5209G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000650458.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 786,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000654076.1",
"gene_hgnc_id": 49761,
"gene_symbol": "LURAP1L-AS1",
"hgvs_c": "n.159-3938G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000654076.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 483,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000803542.1",
"gene_hgnc_id": 49761,
"gene_symbol": "LURAP1L-AS1",
"hgvs_c": "n.309+54988G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000803542.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 501,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000803544.1",
"gene_hgnc_id": 49761,
"gene_symbol": "LURAP1L-AS1",
"hgvs_c": "n.100-16014G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000803544.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 944,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_125775.1",
"gene_hgnc_id": 49761,
"gene_symbol": "LURAP1L-AS1",
"hgvs_c": "n.317-3938G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_125775.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs121912778",
"effect": "stop_gained",
"frequency_reference_population": 0.000048363516,
"gene_hgnc_id": 12450,
"gene_symbol": "TYRP1",
"gnomad_exomes_ac": 69,
"gnomad_exomes_af": 0.0000472344,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 9,
"gnomad_genomes_af": 0.000059216,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "not provided|Oculocutaneous albinism type 3|Oculocutaneous albinism type 3;MELANESIAN BLOND HAIR",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.01,
"pos": 12704564,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000550.3"
}
]
}