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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: 1-92476090-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=92476090&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 92476090,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005263.5",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "NM_005263.5",
"protein_id": "NP_005254.2",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000294702.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005263.5"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "ENST00000294702.6",
"protein_id": "ENSP00000294702.5",
"transcript_support_level": 2,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005263.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000294702.6"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "ENST00000370332.5",
"protein_id": "ENSP00000359357.1",
"transcript_support_level": 1,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370332.5"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "ENST00000427103.6",
"protein_id": "ENSP00000399719.1",
"transcript_support_level": 1,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427103.6"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "NM_001127215.3",
"protein_id": "NP_001120687.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001127215.3"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "NM_001127216.3",
"protein_id": "NP_001120688.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001127216.3"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "ENST00000881421.1",
"protein_id": "ENSP00000551480.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881421.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "ENST00000881422.1",
"protein_id": "ENSP00000551481.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881422.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"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": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.256A>G",
"hgvs_p": "p.Arg86Gly",
"transcript": "ENST00000696667.1",
"protein_id": "ENSP00000512792.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 138,
"cds_start": 256,
"cds_end": null,
"cds_length": 417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696667.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "XM_005270749.4",
"protein_id": "XP_005270806.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005270749.4"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "XM_011541245.3",
"protein_id": "XP_011539547.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541245.3"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg",
"transcript": "XM_011541246.3",
"protein_id": "XP_011539548.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 422,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541246.3"
}
],
"gene_symbol": "GFI1",
"gene_hgnc_id": 4237,
"dbsnp": "rs28936382",
"frequency_reference_population": 0.000057615962,
"hom_count_reference_population": 0,
"allele_count_reference_population": 93,
"gnomad_exomes_af": 0.000058148,
"gnomad_genomes_af": 0.0000525107,
"gnomad_exomes_ac": 85,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.715361475944519,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.317,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2112,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.919,
"phylop100way_prediction": "Uncertain_significance",
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_005263.5",
"gene_symbol": "GFI1",
"hgnc_id": 4237,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1208A>G",
"hgvs_p": "p.Lys403Arg"
}
],
"clinvar_disease": " 2, autosomal dominant, severe congenital,Neutropenia,Nonimmune chronic idiopathic neutropenia of adults",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Nonimmune chronic idiopathic neutropenia of adults|Neutropenia, severe congenital, 2, autosomal dominant",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}