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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: 3-128486911-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=128486911&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 128486911,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000341105.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "NM_032638.5",
"protein_id": "NP_116027.2",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 480,
"cds_start": 121,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 469,
"cdna_end": null,
"cdna_length": 3383,
"mane_select": "ENST00000341105.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "ENST00000341105.7",
"protein_id": "ENSP00000345681.2",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 480,
"cds_start": 121,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 469,
"cdna_end": null,
"cdna_length": 3383,
"mane_select": "NM_032638.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "ENST00000487848.6",
"protein_id": "ENSP00000417074.1",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 480,
"cds_start": 121,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "ENST00000430265.6",
"protein_id": "ENSP00000400259.2",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 466,
"cds_start": 121,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 372,
"cdna_end": null,
"cdna_length": 2525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.403C>G",
"hgvs_p": "p.Pro135Ala",
"transcript": "ENST00000696466.1",
"protein_id": "ENSP00000512647.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 574,
"cds_start": 403,
"cds_end": null,
"cds_length": 1725,
"cdna_start": 884,
"cdna_end": null,
"cdna_length": 3798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "NM_001145661.2",
"protein_id": "NP_001139133.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 480,
"cds_start": 121,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "NM_001145662.1",
"protein_id": "NP_001139134.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 466,
"cds_start": 121,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 377,
"cdna_end": null,
"cdna_length": 3254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "ENST00000492608.1",
"protein_id": "ENSP00000418132.1",
"transcript_support_level": 3,
"aa_start": 41,
"aa_end": null,
"aa_length": 149,
"cds_start": 121,
"cds_end": null,
"cds_length": 450,
"cdna_start": 515,
"cdna_end": null,
"cdna_length": 844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "ENST00000696652.1",
"protein_id": "ENSP00000512781.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 75,
"cds_start": 121,
"cds_end": null,
"cds_length": 229,
"cdna_start": 345,
"cdna_end": null,
"cdna_length": 453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "ENST00000696653.1",
"protein_id": "ENSP00000512782.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 75,
"cds_start": 121,
"cds_end": null,
"cds_length": 229,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "ENST00000696654.1",
"protein_id": "ENSP00000512783.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 75,
"cds_start": 121,
"cds_end": null,
"cds_length": 229,
"cdna_start": 1007,
"cdna_end": null,
"cdna_length": 1115,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala",
"transcript": "ENST00000696661.1",
"protein_id": "ENSP00000512787.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 75,
"cds_start": 121,
"cds_end": null,
"cds_length": 229,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"hgvs_c": "c.*97C>G",
"hgvs_p": null,
"transcript": "ENST00000498200.1",
"protein_id": "ENSP00000419532.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 7,
"cds_start": -4,
"cds_end": null,
"cds_length": 24,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GATA2",
"gene_hgnc_id": 4171,
"dbsnp": "rs143590990",
"frequency_reference_population": 0.00071301556,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1150,
"gnomad_exomes_af": 0.000735371,
"gnomad_genomes_af": 0.000498753,
"gnomad_exomes_ac": 1074,
"gnomad_genomes_ac": 76,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2828771471977234,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.722,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2877,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.556,
"phylop100way_prediction": "Pathogenic",
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000341105.7",
"gene_symbol": "GATA2",
"hgnc_id": 4171,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.121C>G",
"hgvs_p": "p.Pro41Ala"
}
],
"clinvar_disease": "Deafness-lymphedema-leukemia syndrome,GATA2-related disorder,Hereditary cancer-predisposing syndrome,Inborn genetic diseases,Monocytopenia with susceptibility to infections,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:4 B:2",
"phenotype_combined": "not provided|not specified|Deafness-lymphedema-leukemia syndrome;Monocytopenia with susceptibility to infections|Deafness-lymphedema-leukemia syndrome|Hereditary cancer-predisposing syndrome|Monocytopenia with susceptibility to infections|GATA2-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}