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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: 2-38071251-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=38071251&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 38071251,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000104.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "NM_000104.4",
"protein_id": "NP_000095.2",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000610745.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000104.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000610745.5",
"protein_id": "ENSP00000478561.1",
"transcript_support_level": 1,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000104.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000610745.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000490576.2",
"protein_id": "ENSP00000478839.2",
"transcript_support_level": 4,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000490576.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000614273.1",
"protein_id": "ENSP00000483678.1",
"transcript_support_level": 5,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000614273.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000714520.1",
"protein_id": "ENSP00000519767.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714520.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000860003.1",
"protein_id": "ENSP00000530062.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860003.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000948951.1",
"protein_id": "ENSP00000619010.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948951.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000948952.1",
"protein_id": "ENSP00000619011.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948952.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000948953.1",
"protein_id": "ENSP00000619012.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948953.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His",
"transcript": "ENST00000948954.1",
"protein_id": "ENSP00000619013.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 543,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948954.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "c.-11G>A",
"hgvs_p": null,
"transcript": "ENST00000494864.1",
"protein_id": "ENSP00000479876.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": null,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000494864.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "n.481G>A",
"hgvs_p": null,
"transcript": "ENST00000492443.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000492443.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"hgvs_c": "n.498G>A",
"hgvs_p": null,
"transcript": "ENST00000613082.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000613082.1"
}
],
"gene_symbol": "CYP1B1",
"gene_hgnc_id": 2597,
"dbsnp": "rs79204362",
"frequency_reference_population": 0.0031188317,
"hom_count_reference_population": 89,
"allele_count_reference_population": 5031,
"gnomad_exomes_af": 0.00323317,
"gnomad_genomes_af": 0.00202219,
"gnomad_exomes_ac": 4723,
"gnomad_genomes_ac": 308,
"gnomad_exomes_homalt": 87,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009640097618103027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.751,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2003,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.798,
"phylop100way_prediction": "Pathogenic",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PS3,PM1,PM5,PP2,PP3,BP4_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 12,
"pathogenic_score": 10,
"criteria": [
"PS3",
"PM1",
"PM5",
"PP2",
"PP3",
"BP4_Strong",
"BS1",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_000104.4",
"gene_symbol": "CYP1B1",
"hgnc_id": 2597,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368His"
}
],
"clinvar_disease": " 5, B, centronuclear, digenic, early-onset, primary infantile,Anterior segment dysgenesis 6,CYP1B1-related disorder,Congenital glaucoma,Congenital ocular coloboma,Glaucoma,Glaucoma 3,Glaucoma 3A,Irido-corneo-trabecular dysgenesis,Myopathy,Primary congenital glaucoma,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:4 LP:2 US:11 LB:2 B:1 O:1",
"phenotype_combined": "Glaucoma 3A|Glaucoma, early-onset, digenic|not specified|Congenital ocular coloboma|Myopathy, centronuclear, 5|not provided|CYP1B1-related disorder|Irido-corneo-trabecular dysgenesis;Glaucoma 3A|Congenital glaucoma|Primary congenital glaucoma|Anterior segment dysgenesis 6;Glaucoma 3A;Glaucoma 3, primary infantile, B|Anterior segment dysgenesis 6",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}