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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: 4-54265011-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=54265011&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 54265011,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000257290.10",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Glu241Lys",
"transcript": "NM_006206.6",
"protein_id": "NP_006197.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 1089,
"cds_start": 721,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 856,
"cdna_end": null,
"cdna_length": 6378,
"mane_select": "ENST00000257290.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Glu241Lys",
"transcript": "ENST00000257290.10",
"protein_id": "ENSP00000257290.5",
"transcript_support_level": 1,
"aa_start": 241,
"aa_end": null,
"aa_length": 1089,
"cds_start": 721,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 856,
"cdna_end": null,
"cdna_length": 6378,
"mane_select": "NM_006206.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "n.539G>A",
"hgvs_p": null,
"transcript": "ENST00000509092.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2417,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "n.721G>A",
"hgvs_p": null,
"transcript": "ENST00000509490.5",
"protein_id": "ENSP00000424218.1",
"transcript_support_level": 1,
"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": 2991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.*1055G>A",
"hgvs_p": null,
"transcript": "ENST00000508170.5",
"protein_id": "ENSP00000425648.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": -4,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2202,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ENSG00000282278",
"gene_hgnc_id": null,
"hgvs_c": "c.1018-9914G>A",
"hgvs_p": null,
"transcript": "ENST00000507166.5",
"protein_id": "ENSP00000423325.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 849,
"cds_start": -4,
"cds_end": null,
"cds_length": 2550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.796G>A",
"hgvs_p": "p.Glu266Lys",
"transcript": "NM_001347828.2",
"protein_id": "NP_001334757.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 1114,
"cds_start": 796,
"cds_end": null,
"cds_length": 3345,
"cdna_start": 934,
"cdna_end": null,
"cdna_length": 6456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.760G>A",
"hgvs_p": "p.Glu254Lys",
"transcript": "NM_001347830.2",
"protein_id": "NP_001334759.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 1102,
"cds_start": 760,
"cds_end": null,
"cds_length": 3309,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 6794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Glu241Lys",
"transcript": "NM_001347829.2",
"protein_id": "NP_001334758.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 1089,
"cds_start": 721,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 1077,
"cdna_end": null,
"cdna_length": 6599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Glu241Lys",
"transcript": "NM_001347827.2",
"protein_id": "NP_001334756.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 807,
"cds_start": 721,
"cds_end": null,
"cds_length": 2424,
"cdna_start": 856,
"cdna_end": null,
"cdna_length": 2856,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Glu241Lys",
"transcript": "XM_005265743.2",
"protein_id": "XP_005265800.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 1089,
"cds_start": 721,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 1473,
"cdna_end": null,
"cdna_length": 6995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Glu241Lys",
"transcript": "XM_047415766.1",
"protein_id": "XP_047271722.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 1089,
"cds_start": 721,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 936,
"cdna_end": null,
"cdna_length": 6458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Glu241Lys",
"transcript": "XM_047415767.1",
"protein_id": "XP_047271723.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 1089,
"cds_start": 721,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 1239,
"cdna_end": null,
"cdna_length": 6761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.796G>A",
"hgvs_p": "p.Glu266Lys",
"transcript": "XM_006714041.4",
"protein_id": "XP_006714104.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 832,
"cds_start": 796,
"cds_end": null,
"cds_length": 2499,
"cdna_start": 934,
"cdna_end": null,
"cdna_length": 2934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.760G>A",
"hgvs_p": "p.Glu254Lys",
"transcript": "XM_017008281.2",
"protein_id": "XP_016863770.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 820,
"cds_start": 760,
"cds_end": null,
"cds_length": 2463,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 3272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"dbsnp": "rs878854832",
"frequency_reference_population": 6.842154e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84215e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8415659666061401,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.2199999988079071,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.535,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7853,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.765,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.22,
"spliceai_max_prediction": "Uncertain_significance",
"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_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000257290.10",
"gene_symbol": "PDGFRA",
"hgnc_id": 8803,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Glu241Lys"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000507166.5",
"gene_symbol": "ENSG00000282278",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1018-9914G>A",
"hgvs_p": null
}
],
"clinvar_disease": " gastrointestinal, multiple and recurrent inflammatory fibroid,Gastrointestinal stromal tumor,Polyps",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Gastrointestinal stromal tumor|Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}