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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: X-47626062-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=47626062&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 47626062,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000396992.8",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFP",
"gene_hgnc_id": 8864,
"hgvs_c": "c.1240T>G",
"hgvs_p": "p.Tyr414Asp",
"transcript": "NM_001145252.3",
"protein_id": "NP_001138724.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 469,
"cds_start": 1240,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1326,
"cdna_end": null,
"cdna_length": 2489,
"mane_select": "ENST00000396992.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFP",
"gene_hgnc_id": 8864,
"hgvs_c": "c.1240T>G",
"hgvs_p": "p.Tyr414Asp",
"transcript": "ENST00000396992.8",
"protein_id": "ENSP00000380189.3",
"transcript_support_level": 1,
"aa_start": 414,
"aa_end": null,
"aa_length": 469,
"cds_start": 1240,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1326,
"cdna_end": null,
"cdna_length": 2489,
"mane_select": "NM_001145252.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"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": "CFP",
"gene_hgnc_id": 8864,
"hgvs_c": "c.1240T>G",
"hgvs_p": "p.Tyr414Asp",
"transcript": "ENST00000377005.6",
"protein_id": "ENSP00000366204.2",
"transcript_support_level": 1,
"aa_start": 414,
"aa_end": null,
"aa_length": 415,
"cds_start": 1240,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 1435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFP",
"gene_hgnc_id": 8864,
"hgvs_c": "c.1240T>G",
"hgvs_p": "p.Tyr414Asp",
"transcript": "NM_002621.2",
"protein_id": "NP_002612.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 469,
"cds_start": 1240,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1482,
"cdna_end": null,
"cdna_length": 1714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFP",
"gene_hgnc_id": 8864,
"hgvs_c": "c.1240T>G",
"hgvs_p": "p.Tyr414Asp",
"transcript": "ENST00000247153.7",
"protein_id": "ENSP00000247153.3",
"transcript_support_level": 5,
"aa_start": 414,
"aa_end": null,
"aa_length": 469,
"cds_start": 1240,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1482,
"cdna_end": null,
"cdna_length": 1713,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFP",
"gene_hgnc_id": 8864,
"hgvs_c": "n.361T>G",
"hgvs_p": null,
"transcript": "ENST00000478222.1",
"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": 593,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFP",
"gene_hgnc_id": 8864,
"hgvs_c": "n.2537T>G",
"hgvs_p": null,
"transcript": "ENST00000485991.5",
"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": 4040,
"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": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283743",
"gene_hgnc_id": null,
"hgvs_c": "n.1478T>G",
"hgvs_p": null,
"transcript": "ENST00000638776.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 3761,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFP",
"gene_hgnc_id": 8864,
"hgvs_c": "n.1478T>G",
"hgvs_p": null,
"transcript": "ENST00000640573.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 2751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CFP",
"gene_hgnc_id": 8864,
"dbsnp": "rs132630261",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.831640362739563,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.361,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6685,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.287,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000396992.8",
"gene_symbol": "CFP",
"hgnc_id": 8864,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1240T>G",
"hgvs_p": "p.Tyr414Asp"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000638776.2",
"gene_symbol": "ENSG00000283743",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1478T>G",
"hgvs_p": null
}
],
"clinvar_disease": " type III,Properdin deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Properdin deficiency, type III",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}