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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: 5-56882021-TCAA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=56882021&ref=TCAA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 56882021,
"ref": "TCAA",
"alt": "T",
"effect": "conservative_inframe_deletion",
"transcript": "NM_005921.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"hgvs_c": "c.2845_2847delACA",
"hgvs_p": "p.Thr949del",
"transcript": "NM_005921.2",
"protein_id": "NP_005912.1",
"transcript_support_level": null,
"aa_start": 949,
"aa_end": null,
"aa_length": 1512,
"cds_start": 2845,
"cds_end": null,
"cds_length": 4539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000399503.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005921.2"
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"hgvs_c": "c.2845_2847delACA",
"hgvs_p": "p.Thr949del",
"transcript": "ENST00000399503.4",
"protein_id": "ENSP00000382423.3",
"transcript_support_level": 1,
"aa_start": 949,
"aa_end": null,
"aa_length": 1512,
"cds_start": 2845,
"cds_end": null,
"cds_length": 4539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005921.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399503.4"
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"hgvs_c": "c.2839_2841delACA",
"hgvs_p": "p.Thr947del",
"transcript": "ENST00000872825.1",
"protein_id": "ENSP00000542884.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 1510,
"cds_start": 2839,
"cds_end": null,
"cds_length": 4533,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872825.1"
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"hgvs_c": "c.2644_2646delACA",
"hgvs_p": "p.Thr882del",
"transcript": "ENST00000948659.1",
"protein_id": "ENSP00000618718.1",
"transcript_support_level": null,
"aa_start": 882,
"aa_end": null,
"aa_length": 1445,
"cds_start": 2644,
"cds_end": null,
"cds_length": 4338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948659.1"
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"hgvs_c": "c.2566_2568delACA",
"hgvs_p": "p.Thr856del",
"transcript": "ENST00000872824.1",
"protein_id": "ENSP00000542883.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 1419,
"cds_start": 2566,
"cds_end": null,
"cds_length": 4260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872824.1"
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"hgvs_c": "c.2845_2847delACA",
"hgvs_p": "p.Thr949del",
"transcript": "XM_047417218.1",
"protein_id": "XP_047273174.1",
"transcript_support_level": null,
"aa_start": 949,
"aa_end": null,
"aa_length": 1382,
"cds_start": 2845,
"cds_end": null,
"cds_length": 4149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417218.1"
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"hgvs_c": "c.2434_2436delACA",
"hgvs_p": "p.Thr812del",
"transcript": "XM_047417219.1",
"protein_id": "XP_047273175.1",
"transcript_support_level": null,
"aa_start": 812,
"aa_end": null,
"aa_length": 1375,
"cds_start": 2434,
"cds_end": null,
"cds_length": 4128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417219.1"
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"hgvs_c": "c.2434_2436delACA",
"hgvs_p": "p.Thr812del",
"transcript": "XM_047417220.1",
"protein_id": "XP_047273176.1",
"transcript_support_level": null,
"aa_start": 812,
"aa_end": null,
"aa_length": 1375,
"cds_start": 2434,
"cds_end": null,
"cds_length": 4128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417220.1"
}
],
"gene_symbol": "MAP3K1",
"gene_hgnc_id": 6848,
"dbsnp": "rs5868032",
"frequency_reference_population": 0.7699049,
"hom_count_reference_population": 459174,
"allele_count_reference_population": 1209844,
"gnomad_exomes_af": 0.769807,
"gnomad_genomes_af": 0.770831,
"gnomad_exomes_ac": 1093464,
"gnomad_genomes_ac": 116380,
"gnomad_exomes_homalt": 413996,
"gnomad_genomes_homalt": 45178,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 3.282,
"phylop100way_prediction": "Benign",
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_005921.2",
"gene_symbol": "MAP3K1",
"hgnc_id": 6848,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2845_2847delACA",
"hgvs_p": "p.Thr949del"
}
],
"clinvar_disease": "46,XY sex reversal 6,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not specified|46,XY sex reversal 6",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}