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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: 4-56966677-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56966677&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 56966677,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000640343.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "REST",
"gene_hgnc_id": 9966,
"hgvs_c": "c.1004G>C",
"hgvs_p": "p.Arg335Thr",
"transcript": "ENST00000640343.2",
"protein_id": "ENSP00000492813.1",
"transcript_support_level": 1,
"aa_start": 335,
"aa_end": null,
"aa_length": 335,
"cds_start": 1004,
"cds_end": null,
"cds_length": 1008,
"cdna_start": 1133,
"cdna_end": null,
"cdna_length": 1264,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640343.2"
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "REST",
"gene_hgnc_id": 9966,
"hgvs_c": "c.920G>C",
"hgvs_p": "p.Arg307Thr",
"transcript": "ENST00000640168.2",
"protein_id": "ENSP00000490969.1",
"transcript_support_level": 1,
"aa_start": 307,
"aa_end": null,
"aa_length": 307,
"cds_start": 920,
"cds_end": null,
"cds_length": 924,
"cdna_start": 1267,
"cdna_end": null,
"cdna_length": 1328,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640168.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOA1",
"gene_hgnc_id": 28473,
"hgvs_c": "c.1707C>G",
"hgvs_p": "p.Thr569Thr",
"transcript": "NM_032313.4",
"protein_id": "NP_115689.1",
"transcript_support_level": null,
"aa_start": 569,
"aa_end": null,
"aa_length": 698,
"cds_start": 1707,
"cds_end": null,
"cds_length": 2097,
"cdna_start": 1728,
"cdna_end": null,
"cdna_length": 2218,
"mane_select": "ENST00000264230.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032313.4"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOA1",
"gene_hgnc_id": 28473,
"hgvs_c": "c.1707C>G",
"hgvs_p": "p.Thr569Thr",
"transcript": "ENST00000264230.5",
"protein_id": "ENSP00000264230.4",
"transcript_support_level": 1,
"aa_start": 569,
"aa_end": null,
"aa_length": 698,
"cds_start": 1707,
"cds_end": null,
"cds_length": 2097,
"cdna_start": 1728,
"cdna_end": null,
"cdna_length": 2218,
"mane_select": "NM_032313.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264230.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOA1",
"gene_hgnc_id": 28473,
"hgvs_c": "c.1731C>G",
"hgvs_p": "p.Thr577Thr",
"transcript": "ENST00000904433.1",
"protein_id": "ENSP00000574492.1",
"transcript_support_level": null,
"aa_start": 577,
"aa_end": null,
"aa_length": 706,
"cds_start": 1731,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 1739,
"cdna_end": null,
"cdna_length": 2231,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904433.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOA1",
"gene_hgnc_id": 28473,
"hgvs_c": "c.1698C>G",
"hgvs_p": "p.Thr566Thr",
"transcript": "ENST00000904430.1",
"protein_id": "ENSP00000574489.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 695,
"cds_start": 1698,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1718,
"cdna_end": null,
"cdna_length": 2211,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904430.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOA1",
"gene_hgnc_id": 28473,
"hgvs_c": "c.1656C>G",
"hgvs_p": "p.Thr552Thr",
"transcript": "ENST00000904431.1",
"protein_id": "ENSP00000574490.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 681,
"cds_start": 1656,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 1676,
"cdna_end": null,
"cdna_length": 2164,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904431.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOA1",
"gene_hgnc_id": 28473,
"hgvs_c": "c.1575C>G",
"hgvs_p": "p.Thr525Thr",
"transcript": "ENST00000933297.1",
"protein_id": "ENSP00000603356.1",
"transcript_support_level": null,
"aa_start": 525,
"aa_end": null,
"aa_length": 654,
"cds_start": 1575,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1595,
"cdna_end": null,
"cdna_length": 2559,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933297.1"
},
{
"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": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NOA1",
"gene_hgnc_id": 28473,
"hgvs_c": "c.1647+1707C>G",
"hgvs_p": null,
"transcript": "ENST00000904429.1",
"protein_id": "ENSP00000574488.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 659,
"cds_start": null,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2590,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904429.1"
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NOA1",
"gene_hgnc_id": 28473,
"hgvs_c": "c.1516-2151C>G",
"hgvs_p": null,
"transcript": "ENST00000904432.1",
"protein_id": "ENSP00000574491.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 615,
"cds_start": null,
"cds_end": null,
"cds_length": 1848,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1965,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904432.1"
}
],
"gene_symbol": "REST",
"gene_hgnc_id": 9966,
"dbsnp": "rs369847942",
"frequency_reference_population": 0.000050809733,
"hom_count_reference_population": 1,
"allele_count_reference_population": 82,
"gnomad_exomes_af": 0.0000492581,
"gnomad_genomes_af": 0.0000657134,
"gnomad_exomes_ac": 72,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11834996938705444,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"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": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.957,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000640343.2",
"gene_symbol": "REST",
"hgnc_id": 9966,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1004G>C",
"hgvs_p": "p.Arg335Thr"
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_032313.4",
"gene_symbol": "NOA1",
"hgnc_id": 28473,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1707C>G",
"hgvs_p": "p.Thr569Thr"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}