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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: 2-25742226-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=25742226&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 25742226,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018263.6",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASXL2",
"gene_hgnc_id": 23805,
"hgvs_c": "c.4111C>A",
"hgvs_p": "p.Gln1371Lys",
"transcript": "NM_018263.6",
"protein_id": "NP_060733.4",
"transcript_support_level": null,
"aa_start": 1371,
"aa_end": null,
"aa_length": 1435,
"cds_start": 4111,
"cds_end": null,
"cds_length": 4308,
"cdna_start": 4376,
"cdna_end": null,
"cdna_length": 12849,
"mane_select": "ENST00000435504.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018263.6"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASXL2",
"gene_hgnc_id": 23805,
"hgvs_c": "c.4111C>A",
"hgvs_p": "p.Gln1371Lys",
"transcript": "ENST00000435504.9",
"protein_id": "ENSP00000391447.3",
"transcript_support_level": 5,
"aa_start": 1371,
"aa_end": null,
"aa_length": 1435,
"cds_start": 4111,
"cds_end": null,
"cds_length": 4308,
"cdna_start": 4376,
"cdna_end": null,
"cdna_length": 12849,
"mane_select": "NM_018263.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000435504.9"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASXL2",
"gene_hgnc_id": 23805,
"hgvs_c": "c.4108C>A",
"hgvs_p": "p.Gln1370Lys",
"transcript": "ENST00000336112.9",
"protein_id": "ENSP00000337250.5",
"transcript_support_level": 1,
"aa_start": 1370,
"aa_end": null,
"aa_length": 1434,
"cds_start": 4108,
"cds_end": null,
"cds_length": 4305,
"cdna_start": 4352,
"cdna_end": null,
"cdna_length": 8886,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000336112.9"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASXL2",
"gene_hgnc_id": 23805,
"hgvs_c": "c.2560C>A",
"hgvs_p": "p.Gln854Lys",
"transcript": "ENST00000404843.5",
"protein_id": "ENSP00000383920.1",
"transcript_support_level": 1,
"aa_start": 854,
"aa_end": null,
"aa_length": 918,
"cds_start": 2560,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 2998,
"cdna_end": null,
"cdna_length": 3299,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000404843.5"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASXL2",
"gene_hgnc_id": 23805,
"hgvs_c": "c.3937C>A",
"hgvs_p": "p.Gln1313Lys",
"transcript": "NM_001369346.1",
"protein_id": "NP_001356275.1",
"transcript_support_level": null,
"aa_start": 1313,
"aa_end": null,
"aa_length": 1377,
"cds_start": 3937,
"cds_end": null,
"cds_length": 4134,
"cdna_start": 4059,
"cdna_end": null,
"cdna_length": 12532,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001369346.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASXL2",
"gene_hgnc_id": 23805,
"hgvs_c": "c.3331C>A",
"hgvs_p": "p.Gln1111Lys",
"transcript": "NM_001369347.1",
"protein_id": "NP_001356276.1",
"transcript_support_level": null,
"aa_start": 1111,
"aa_end": null,
"aa_length": 1175,
"cds_start": 3331,
"cds_end": null,
"cds_length": 3528,
"cdna_start": 3994,
"cdna_end": null,
"cdna_length": 12467,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001369347.1"
}
],
"gene_symbol": "ASXL2",
"gene_hgnc_id": 23805,
"dbsnp": "rs115221221",
"frequency_reference_population": 0.0036369765,
"hom_count_reference_population": 35,
"allele_count_reference_population": 5870,
"gnomad_exomes_af": 0.00362044,
"gnomad_genomes_af": 0.00379569,
"gnomad_exomes_ac": 5292,
"gnomad_genomes_ac": 578,
"gnomad_exomes_homalt": 29,
"gnomad_genomes_homalt": 6,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005208849906921387,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.147,
"revel_prediction": "Benign",
"alphamissense_score": 0.1262,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.274,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_018263.6",
"gene_symbol": "ASXL2",
"hgnc_id": 23805,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4111C>A",
"hgvs_p": "p.Gln1371Lys"
}
],
"clinvar_disease": "Shashi-Pena syndrome,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:2",
"phenotype_combined": "not provided|Shashi-Pena syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}