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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: 1-109690516-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=109690516&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 109690516,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000309851.10",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.519G>A",
"hgvs_p": "p.Lys173Lys",
"transcript": "NM_000561.4",
"protein_id": "NP_000552.2",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 218,
"cds_start": 519,
"cds_end": null,
"cds_length": 657,
"cdna_start": 576,
"cdna_end": null,
"cdna_length": 1164,
"mane_select": "ENST00000309851.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.519G>A",
"hgvs_p": "p.Lys173Lys",
"transcript": "ENST00000309851.10",
"protein_id": "ENSP00000311469.5",
"transcript_support_level": 1,
"aa_start": 173,
"aa_end": null,
"aa_length": 218,
"cds_start": 519,
"cds_end": null,
"cds_length": 657,
"cdna_start": 576,
"cdna_end": null,
"cdna_length": 1164,
"mane_select": "NM_000561.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.456+150G>A",
"hgvs_p": null,
"transcript": "ENST00000349334.7",
"protein_id": "ENSP00000234981.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 181,
"cds_start": -4,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.360+1191G>A",
"hgvs_p": null,
"transcript": "ENST00000369819.2",
"protein_id": "ENSP00000358834.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 149,
"cds_start": -4,
"cds_end": null,
"cds_length": 450,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.576G>A",
"hgvs_p": "p.Lys192Lys",
"transcript": "ENST00000369823.6",
"protein_id": "ENSP00000358838.2",
"transcript_support_level": 3,
"aa_start": 192,
"aa_end": null,
"aa_length": 237,
"cds_start": 576,
"cds_end": null,
"cds_length": 714,
"cdna_start": 621,
"cdna_end": null,
"cdna_length": 852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.417G>A",
"hgvs_p": "p.Lys139Lys",
"transcript": "XM_005270782.6",
"protein_id": "XP_005270839.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 184,
"cds_start": 417,
"cds_end": null,
"cds_length": 555,
"cdna_start": 629,
"cdna_end": null,
"cdna_length": 1217,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "GSTM2",
"gene_hgnc_id": 4634,
"hgvs_c": "c.568-17965G>A",
"hgvs_p": null,
"transcript": "ENST00000369831.6",
"protein_id": "ENSP00000358846.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 220,
"cds_start": -4,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "GSTM2",
"gene_hgnc_id": 4634,
"hgvs_c": "c.*17+8682G>A",
"hgvs_p": null,
"transcript": "ENST00000460717.8",
"protein_id": "ENSP00000435910.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 191,
"cds_start": -4,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.456+150G>A",
"hgvs_p": null,
"transcript": "NM_146421.3",
"protein_id": "NP_666533.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 181,
"cds_start": -4,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.*20+1191G>A",
"hgvs_p": null,
"transcript": "ENST00000483399.6",
"protein_id": "ENSP00000455929.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 85,
"cds_start": -4,
"cds_end": null,
"cds_length": 258,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "n.344+1191G>A",
"hgvs_p": null,
"transcript": "ENST00000490021.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 903,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"hgvs_c": "c.*197G>A",
"hgvs_p": null,
"transcript": "ENST00000476065.6",
"protein_id": "ENSP00000456315.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 101,
"cds_start": -4,
"cds_end": null,
"cds_length": 307,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 491,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GSTM1",
"gene_hgnc_id": 4632,
"dbsnp": "rs1065411",
"frequency_reference_population": null,
"hom_count_reference_population": null,
"allele_count_reference_population": null,
"gnomad_exomes_af": 0.00000280229,
"gnomad_genomes_af": 0,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 0,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8799999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.88,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.057,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000309851.10",
"gene_symbol": "GSTM1",
"hgnc_id": 4632,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.519G>A",
"hgvs_p": "p.Lys173Lys"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000369831.6",
"gene_symbol": "GSTM2",
"hgnc_id": 4634,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.568-17965G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}