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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: 3-128481938-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=128481938&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 128481938,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000341105.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"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.1024G>A",
"hgvs_p": "p.Ala342Thr",
"transcript": "NM_001145661.2",
"protein_id": "NP_001139133.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 480,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1459,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": null,
"mane_plus": "ENST00000487848.6",
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"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.1024G>A",
"hgvs_p": "p.Ala342Thr",
"transcript": "NM_032638.5",
"protein_id": "NP_116027.2",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 480,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1372,
"cdna_end": null,
"cdna_length": 3383,
"mane_select": "ENST00000341105.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"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.1024G>A",
"hgvs_p": "p.Ala342Thr",
"transcript": "ENST00000341105.7",
"protein_id": "ENSP00000345681.2",
"transcript_support_level": 1,
"aa_start": 342,
"aa_end": null,
"aa_length": 480,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1372,
"cdna_end": null,
"cdna_length": 3383,
"mane_select": "NM_032638.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"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.1024G>A",
"hgvs_p": "p.Ala342Thr",
"transcript": "ENST00000487848.6",
"protein_id": "ENSP00000417074.1",
"transcript_support_level": 1,
"aa_start": 342,
"aa_end": null,
"aa_length": 480,
"cds_start": 1024,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1459,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": null,
"mane_plus": "NM_001145661.2",
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1018-36G>A",
"hgvs_p": null,
"transcript": "ENST00000430265.6",
"protein_id": "ENSP00000400259.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 466,
"cds_start": -4,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"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.1306G>A",
"hgvs_p": "p.Ala436Thr",
"transcript": "ENST00000696466.1",
"protein_id": "ENSP00000512647.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 574,
"cds_start": 1306,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 1787,
"cdna_end": null,
"cdna_length": 3798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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": "c.7G>A",
"hgvs_p": "p.Ala3Thr",
"transcript": "ENST00000696672.1",
"protein_id": "ENSP00000512796.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 192,
"cds_start": 7,
"cds_end": null,
"cds_length": 579,
"cdna_start": 7,
"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.141G>A",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.1018-36G>A",
"hgvs_p": null,
"transcript": "NM_001145662.1",
"protein_id": "NP_001139134.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 466,
"cds_start": -4,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"dbsnp": "rs751285156",
"frequency_reference_population": 0.000021693802,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000212156,
"gnomad_genomes_af": 0.0000262857,
"gnomad_exomes_ac": 31,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7825847864151001,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.524,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8686,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.934,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM1,PP3,BS2",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 4,
"pathogenic_score": 3,
"criteria": [
"PM1",
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000341105.7",
"gene_symbol": "GATA2",
"hgnc_id": 4171,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1024G>A",
"hgvs_p": "p.Ala342Thr"
}
],
"clinvar_disease": "Acute myeloid leukemia,Deafness-lymphedema-leukemia syndrome,GATA2 deficiency with susceptibility to MDS/AML,Inborn genetic diseases,Monocytopenia with susceptibility to infections,Myelodysplastic syndrome,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:7",
"phenotype_combined": "Monocytopenia with susceptibility to infections;Deafness-lymphedema-leukemia syndrome|GATA2 deficiency with susceptibility to MDS/AML;Deafness-lymphedema-leukemia syndrome|Acute myeloid leukemia|Monocytopenia with susceptibility to infections;Myelodysplastic syndrome;Acute myeloid leukemia;Deafness-lymphedema-leukemia syndrome|not provided|Inborn genetic diseases|Deafness-lymphedema-leukemia syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}