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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: 3-71754179-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=71754179&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 71754179,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_018971.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPR27",
"gene_hgnc_id": 4482,
"hgvs_c": "c.130G>C",
"hgvs_p": "p.Val44Leu",
"transcript": "NM_018971.3",
"protein_id": "NP_061844.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 375,
"cds_start": 130,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000304411.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018971.3"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPR27",
"gene_hgnc_id": 4482,
"hgvs_c": "c.130G>C",
"hgvs_p": "p.Val44Leu",
"transcript": "ENST00000304411.3",
"protein_id": "ENSP00000303149.2",
"transcript_support_level": 6,
"aa_start": 44,
"aa_end": null,
"aa_length": 375,
"cds_start": 130,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018971.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000304411.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285708",
"gene_hgnc_id": null,
"hgvs_c": "c.-959+36C>G",
"hgvs_p": null,
"transcript": "ENST00000647725.1",
"protein_id": "ENSP00000497585.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 677,
"cds_start": null,
"cds_end": null,
"cds_length": 2034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647725.1"
},
{
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EIF4E3",
"gene_hgnc_id": 31837,
"hgvs_c": "c.-291+465C>G",
"hgvs_p": null,
"transcript": "ENST00000421769.6",
"protein_id": "ENSP00000411762.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 118,
"cds_start": null,
"cds_end": null,
"cds_length": 357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421769.6"
},
{
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EIF4E3",
"gene_hgnc_id": 31837,
"hgvs_c": "c.-291+36C>G",
"hgvs_p": null,
"transcript": "NM_001134649.3",
"protein_id": "NP_001128121.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 118,
"cds_start": null,
"cds_end": null,
"cds_length": 357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001134649.3"
},
{
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EIF4E3",
"gene_hgnc_id": 31837,
"hgvs_c": "c.-291+465C>G",
"hgvs_p": null,
"transcript": "NM_173359.5",
"protein_id": "NP_775495.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 118,
"cds_start": null,
"cds_end": null,
"cds_length": 357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_173359.5"
},
{
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EIF4E3",
"gene_hgnc_id": 31837,
"hgvs_c": "c.-291+36C>G",
"hgvs_p": null,
"transcript": "ENST00000448225.5",
"protein_id": "ENSP00000410350.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 118,
"cds_start": null,
"cds_end": null,
"cds_length": 357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000448225.5"
},
{
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EIF4E3",
"gene_hgnc_id": 31837,
"hgvs_c": "c.-291+36C>G",
"hgvs_p": null,
"transcript": "ENST00000496214.6",
"protein_id": "ENSP00000417889.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 50,
"cds_start": null,
"cds_end": null,
"cds_length": 154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000496214.6"
},
{
"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": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EIF4E3",
"gene_hgnc_id": 31837,
"hgvs_c": "c.-413+36C>G",
"hgvs_p": null,
"transcript": "XM_047448063.1",
"protein_id": "XP_047304019.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 118,
"cds_start": null,
"cds_end": null,
"cds_length": 357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448063.1"
}
],
"gene_symbol": "GPR27",
"gene_hgnc_id": 4482,
"dbsnp": "rs758405764",
"frequency_reference_population": 0.00015596492,
"hom_count_reference_population": 0,
"allele_count_reference_population": 225,
"gnomad_exomes_af": 0.000166159,
"gnomad_genomes_af": 0.0000672549,
"gnomad_exomes_ac": 215,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.034168899059295654,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.0706,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.548,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_018971.3",
"gene_symbol": "GPR27",
"hgnc_id": 4482,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.130G>C",
"hgvs_p": "p.Val44Leu"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_173359.5",
"gene_symbol": "EIF4E3",
"hgnc_id": 31837,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-291+465C>G",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000647725.1",
"gene_symbol": "ENSG00000285708",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.-959+36C>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}