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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: 7-99709216-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=99709216&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 99709216,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000765.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A7",
"gene_hgnc_id": 2640,
"hgvs_c": "c.1072A>T",
"hgvs_p": "p.Met358Leu",
"transcript": "NM_000765.5",
"protein_id": "NP_000756.3",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 503,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1175,
"cdna_end": null,
"cdna_length": 2079,
"mane_select": "ENST00000336374.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A7",
"gene_hgnc_id": 2640,
"hgvs_c": "c.1072A>T",
"hgvs_p": "p.Met358Leu",
"transcript": "ENST00000336374.4",
"protein_id": "ENSP00000337450.2",
"transcript_support_level": 1,
"aa_start": 358,
"aa_end": null,
"aa_length": 503,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1175,
"cdna_end": null,
"cdna_length": 2079,
"mane_select": "NM_000765.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A7-CYP3A51P",
"gene_hgnc_id": 51504,
"hgvs_c": "c.1072A>T",
"hgvs_p": "p.Met358Leu",
"transcript": "ENST00000620220.6",
"protein_id": "ENSP00000479282.3",
"transcript_support_level": 1,
"aa_start": 358,
"aa_end": null,
"aa_length": 503,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1081,
"cdna_end": null,
"cdna_length": 1704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A7-CYP3A51P",
"gene_hgnc_id": 51504,
"hgvs_c": "c.1072A>T",
"hgvs_p": "p.Met358Leu",
"transcript": "NM_001256497.3",
"protein_id": "NP_001243426.2",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 535,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 1175,
"cdna_end": null,
"cdna_length": 2260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A7-CYP3A51P",
"gene_hgnc_id": 51504,
"hgvs_c": "c.1072A>T",
"hgvs_p": "p.Met358Leu",
"transcript": "ENST00000611620.4",
"protein_id": "ENSP00000480571.1",
"transcript_support_level": 5,
"aa_start": 358,
"aa_end": null,
"aa_length": 535,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 1072,
"cdna_end": null,
"cdna_length": 1608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP3A7",
"gene_hgnc_id": 2640,
"hgvs_c": "n.1411A>T",
"hgvs_p": null,
"transcript": "ENST00000477357.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2314,
"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": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ZSCAN25",
"gene_hgnc_id": 21961,
"hgvs_c": "n.1108-14259T>A",
"hgvs_p": null,
"transcript": "XR_007059988.1",
"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": 2772,
"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": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ZSCAN25",
"gene_hgnc_id": 21961,
"hgvs_c": "n.1050-14259T>A",
"hgvs_p": null,
"transcript": "XR_007059989.1",
"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": 2714,
"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": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ZSCAN25",
"gene_hgnc_id": 21961,
"hgvs_c": "n.923-14259T>A",
"hgvs_p": null,
"transcript": "XR_007059990.1",
"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": 2587,
"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": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ZSCAN25",
"gene_hgnc_id": 21961,
"hgvs_c": "n.1135-14259T>A",
"hgvs_p": null,
"transcript": "XR_927402.3",
"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": 2799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CYP3A7",
"gene_hgnc_id": 2640,
"dbsnp": "rs748863341",
"frequency_reference_population": 0.0000013683447,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136834,
"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": 0.4508320987224579,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.266,
"revel_prediction": "Benign",
"alphamissense_score": 0.2873,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.421,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000765.5",
"gene_symbol": "CYP3A7",
"hgnc_id": 2640,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1072A>T",
"hgvs_p": "p.Met358Leu"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000620220.6",
"gene_symbol": "CYP3A7-CYP3A51P",
"hgnc_id": 51504,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1072A>T",
"hgvs_p": "p.Met358Leu"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XR_927402.3",
"gene_symbol": "ZSCAN25",
"hgnc_id": 21961,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.1135-14259T>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
}