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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: 6-131583811-GA-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=131583811&ref=GA&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 131583811,
"ref": "GA",
"alt": "G",
"effect": "frameshift_variant",
"transcript": "ENST00000368087.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.874delA",
"hgvs_p": "p.Thr292fs",
"transcript": "NM_000045.4",
"protein_id": "NP_000036.2",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 322,
"cds_start": 874,
"cds_end": null,
"cds_length": 969,
"cdna_start": 931,
"cdna_end": null,
"cdna_length": 1447,
"mane_select": "ENST00000368087.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.874delA",
"hgvs_p": "p.Thr292fs",
"transcript": "ENST00000368087.8",
"protein_id": "ENSP00000357066.3",
"transcript_support_level": 1,
"aa_start": 292,
"aa_end": null,
"aa_length": 322,
"cds_start": 874,
"cds_end": null,
"cds_length": 969,
"cdna_start": 931,
"cdna_end": null,
"cdna_length": 1447,
"mane_select": "NM_000045.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.898delA",
"hgvs_p": "p.Thr300fs",
"transcript": "ENST00000356962.2",
"protein_id": "ENSP00000349446.2",
"transcript_support_level": 1,
"aa_start": 300,
"aa_end": null,
"aa_length": 330,
"cds_start": 898,
"cds_end": null,
"cds_length": 993,
"cdna_start": 956,
"cdna_end": null,
"cdna_length": 1468,
"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": 31,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "MED23",
"gene_hgnc_id": 2372,
"hgvs_c": "c.4095+3897delT",
"hgvs_p": null,
"transcript": "ENST00000354577.8",
"protein_id": "ENSP00000346588.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1365,
"cds_start": -4,
"cds_end": null,
"cds_length": 4098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.898delA",
"hgvs_p": "p.Thr300fs",
"transcript": "NM_001244438.2",
"protein_id": "NP_001231367.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 330,
"cds_start": 898,
"cds_end": null,
"cds_length": 993,
"cdna_start": 955,
"cdna_end": null,
"cdna_length": 1471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.820delA",
"hgvs_p": "p.Thr274fs",
"transcript": "ENST00000672233.1",
"protein_id": "ENSP00000499826.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 304,
"cds_start": 820,
"cds_end": null,
"cds_length": 915,
"cdna_start": 894,
"cdna_end": null,
"cdna_length": 1059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.619delA",
"hgvs_p": "p.Thr207fs",
"transcript": "NM_001369020.1",
"protein_id": "NP_001355949.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 237,
"cds_start": 619,
"cds_end": null,
"cds_length": 714,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 1192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.619delA",
"hgvs_p": "p.Thr207fs",
"transcript": "ENST00000673427.1",
"protein_id": "ENSP00000500160.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 237,
"cds_start": 619,
"cds_end": null,
"cds_length": 714,
"cdna_start": 673,
"cdna_end": null,
"cdna_length": 1192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "n.*761delA",
"hgvs_p": null,
"transcript": "ENST00000673234.1",
"protein_id": "ENSP00000499885.1",
"transcript_support_level": null,
"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": 1230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "n.858delA",
"hgvs_p": null,
"transcript": "NR_160934.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "n.*761delA",
"hgvs_p": null,
"transcript": "ENST00000673234.1",
"protein_id": "ENSP00000499885.1",
"transcript_support_level": null,
"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": 1230,
"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": 31,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "MED23",
"gene_hgnc_id": 2372,
"hgvs_c": "c.4095+3897delT",
"hgvs_p": null,
"transcript": "NM_015979.4",
"protein_id": "NP_057063.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1365,
"cds_start": -4,
"cds_end": null,
"cds_length": 4098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4618,
"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": 30,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "MED23",
"gene_hgnc_id": 2372,
"hgvs_c": "c.4077+3897delT",
"hgvs_p": null,
"transcript": "NM_001270521.2",
"protein_id": "NP_001257450.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1359,
"cds_start": -4,
"cds_end": null,
"cds_length": 4080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"dbsnp": "rs771395982",
"frequency_reference_population": 0.0000013681856,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136819,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"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": -0.766,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000368087.8",
"gene_symbol": "ARG1",
"hgnc_id": 663,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.874delA",
"hgvs_p": "p.Thr292fs"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_015979.4",
"gene_symbol": "MED23",
"hgnc_id": 2372,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4095+3897delT",
"hgvs_p": null
}
],
"clinvar_disease": "Arginase deficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Arginase deficiency",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}