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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: 1-109713539-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=109713539&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GSTM5",
"hgnc_id": 4637,
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_000851.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 40,
"alphamissense_prediction": null,
"alphamissense_score": 0.3037,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.31,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.7412533760070801,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 218,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1561,
"cdna_start": 295,
"cds_end": null,
"cds_length": 657,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_000851.4",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000256593.8",
"protein_coding": true,
"protein_id": "NP_000842.2",
"strand": true,
"transcript": "NM_000851.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 218,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1561,
"cdna_start": 295,
"cds_end": null,
"cds_length": 657,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000256593.8",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000851.4",
"protein_coding": true,
"protein_id": "ENSP00000256593.3",
"strand": true,
"transcript": "ENST00000256593.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 244,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1199,
"cdna_start": 283,
"cds_end": null,
"cds_length": 735,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000878690.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548749.1",
"strand": true,
"transcript": "ENST00000878690.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 244,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1672,
"cdna_start": 335,
"cds_end": null,
"cds_length": 735,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000966870.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636929.1",
"strand": true,
"transcript": "ENST00000966870.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 218,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 657,
"cdna_start": 233,
"cds_end": null,
"cds_length": 657,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000369812.6",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358827.5",
"strand": true,
"transcript": "ENST00000369812.6",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 217,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1568,
"cdna_start": 307,
"cds_end": null,
"cds_length": 654,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000966873.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636932.1",
"strand": true,
"transcript": "ENST00000966873.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 188,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 635,
"cdna_start": 301,
"cds_end": null,
"cds_length": 567,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000647711.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496849.1",
"strand": true,
"transcript": "ENST00000647711.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 171,
"aa_ref": "R",
"aa_start": 31,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 978,
"cdna_start": 142,
"cds_end": null,
"cds_length": 516,
"cds_start": 92,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000966874.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636933.1",
"strand": true,
"transcript": "ENST00000966874.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 149,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 926,
"cdna_start": 290,
"cds_end": null,
"cds_length": 450,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000878689.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548748.1",
"strand": true,
"transcript": "ENST00000878689.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 218,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1596,
"cdna_start": 330,
"cds_end": null,
"cds_length": 657,
"cds_start": 233,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_005270784.5",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.233G>A",
"hgvs_p": "p.Arg78His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005270841.1",
"strand": true,
"transcript": "XM_005270784.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 169,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 990,
"cdna_start": null,
"cds_end": null,
"cds_length": 510,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000966872.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.113-122G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636931.1",
"strand": true,
"transcript": "ENST00000966872.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 157,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1386,
"cdna_start": null,
"cds_end": null,
"cds_length": 474,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000878688.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.177+356G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548747.1",
"strand": true,
"transcript": "ENST00000878688.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 110,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1311,
"cdna_start": null,
"cds_end": null,
"cds_length": 333,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000966871.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.36+1191G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636930.1",
"strand": true,
"transcript": "ENST00000966871.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 41,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 572,
"cdna_start": null,
"cds_end": null,
"cds_length": 126,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000878691.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.36+1191G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548750.1",
"strand": true,
"transcript": "ENST00000878691.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 114,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1311,
"cdna_start": null,
"cds_end": null,
"cds_length": 345,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005270785.5",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.-53-122G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005270842.1",
"strand": true,
"transcript": "XM_005270785.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4370,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000369813.5",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "n.1015G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000369813.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 439,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000429410.2",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "n.82+1191G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000429410.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 109,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 720,
"cdna_start": null,
"cds_end": null,
"cds_length": 330,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648974.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "c.-196G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000498086.1",
"strand": true,
"transcript": "ENST00000648974.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4208,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000492718.1",
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"hgvs_c": "n.-5G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000492718.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs750371938",
"effect": "missense_variant",
"frequency_reference_population": 0.000024781888,
"gene_hgnc_id": 4637,
"gene_symbol": "GSTM5",
"gnomad_exomes_ac": 34,
"gnomad_exomes_af": 0.0000232575,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.0000394249,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.347,
"pos": 109713539,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.308,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000851.4"
}
]
}