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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: 3-128481878-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=128481878&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 128481878,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000341105.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1084C>T",
"hgvs_p": "p.Arg362*",
"transcript": "NM_032638.5",
"protein_id": "NP_116027.2",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 480,
"cds_start": 1084,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 3383,
"mane_select": "ENST00000341105.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1084C>T",
"hgvs_p": "p.Arg362*",
"transcript": "ENST00000341105.7",
"protein_id": "ENSP00000345681.2",
"transcript_support_level": 1,
"aa_start": 362,
"aa_end": null,
"aa_length": 480,
"cds_start": 1084,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 3383,
"mane_select": "NM_032638.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1084C>T",
"hgvs_p": "p.Arg362*",
"transcript": "ENST00000487848.6",
"protein_id": "ENSP00000417074.1",
"transcript_support_level": 1,
"aa_start": 362,
"aa_end": null,
"aa_length": 480,
"cds_start": 1084,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1519,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1042C>T",
"hgvs_p": "p.Arg348*",
"transcript": "ENST00000430265.6",
"protein_id": "ENSP00000400259.2",
"transcript_support_level": 1,
"aa_start": 348,
"aa_end": null,
"aa_length": 466,
"cds_start": 1042,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 1293,
"cdna_end": null,
"cdna_length": 2525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1366C>T",
"hgvs_p": "p.Arg456*",
"transcript": "ENST00000696466.1",
"protein_id": "ENSP00000512647.1",
"transcript_support_level": null,
"aa_start": 456,
"aa_end": null,
"aa_length": 574,
"cds_start": 1366,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 3798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1084C>T",
"hgvs_p": "p.Arg362*",
"transcript": "NM_001145661.2",
"protein_id": "NP_001139133.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 480,
"cds_start": 1084,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1519,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1042C>T",
"hgvs_p": "p.Arg348*",
"transcript": "NM_001145662.1",
"protein_id": "NP_001139134.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 466,
"cds_start": 1042,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 1298,
"cdna_end": null,
"cdna_length": 3254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.67C>T",
"hgvs_p": "p.Arg23*",
"transcript": "ENST00000696672.1",
"protein_id": "ENSP00000512796.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 192,
"cds_start": 67,
"cds_end": null,
"cds_length": 579,
"cdna_start": 67,
"cdna_end": null,
"cdna_length": 2010,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "n.201C>T",
"hgvs_p": null,
"transcript": "ENST00000489987.1",
"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": 1433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"dbsnp": "rs1553770510",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5400000214576721,
"computational_prediction_selected": "Pathogenic",
"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": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.64,
"phylop100way_prediction": "Uncertain_significance",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000341105.7",
"gene_symbol": "GATA2",
"hgnc_id": 4171,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1084C>T",
"hgvs_p": "p.Arg362*"
}
],
"clinvar_disease": " acute myeloid, susceptibility to,Deafness-lymphedema-leukemia syndrome,GATA2 deficiency with susceptibility to MDS/AML,GATA2-related disorder,Leukemia,Monocytopenia with susceptibility to infections,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8 LP:1",
"phenotype_combined": "Leukemia, acute myeloid, susceptibility to|not provided|Deafness-lymphedema-leukemia syndrome|GATA2 deficiency with susceptibility to MDS/AML;Deafness-lymphedema-leukemia syndrome|Monocytopenia with susceptibility to infections;Deafness-lymphedema-leukemia syndrome|GATA2-related disorder|GATA2 deficiency with susceptibility to MDS/AML",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}