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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: 4-54272475-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=54272475&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 54272475,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000257290.10",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1319C>T",
"hgvs_p": "p.Thr440Met",
"transcript": "NM_006206.6",
"protein_id": "NP_006197.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 1089,
"cds_start": 1319,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 1454,
"cdna_end": null,
"cdna_length": 6378,
"mane_select": "ENST00000257290.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1319C>T",
"hgvs_p": "p.Thr440Met",
"transcript": "ENST00000257290.10",
"protein_id": "ENSP00000257290.5",
"transcript_support_level": 1,
"aa_start": 440,
"aa_end": null,
"aa_length": 1089,
"cds_start": 1319,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 1454,
"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": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "n.1137C>T",
"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": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "n.1319C>T",
"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": 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.1018-2450C>T",
"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": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1394C>T",
"hgvs_p": "p.Thr465Met",
"transcript": "NM_001347828.2",
"protein_id": "NP_001334757.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 1114,
"cds_start": 1394,
"cds_end": null,
"cds_length": 3345,
"cdna_start": 1532,
"cdna_end": null,
"cdna_length": 6456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Thr453Met",
"transcript": "NM_001347830.2",
"protein_id": "NP_001334759.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 1102,
"cds_start": 1358,
"cds_end": null,
"cds_length": 3309,
"cdna_start": 1870,
"cdna_end": null,
"cdna_length": 6794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1319C>T",
"hgvs_p": "p.Thr440Met",
"transcript": "NM_001347829.2",
"protein_id": "NP_001334758.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 1089,
"cds_start": 1319,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 1675,
"cdna_end": null,
"cdna_length": 6599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1319C>T",
"hgvs_p": "p.Thr440Met",
"transcript": "NM_001347827.2",
"protein_id": "NP_001334756.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 807,
"cds_start": 1319,
"cds_end": null,
"cds_length": 2424,
"cdna_start": 1454,
"cdna_end": null,
"cdna_length": 2856,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1319C>T",
"hgvs_p": "p.Thr440Met",
"transcript": "XM_005265743.2",
"protein_id": "XP_005265800.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 1089,
"cds_start": 1319,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 2071,
"cdna_end": null,
"cdna_length": 6995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1319C>T",
"hgvs_p": "p.Thr440Met",
"transcript": "XM_047415766.1",
"protein_id": "XP_047271722.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 1089,
"cds_start": 1319,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 1534,
"cdna_end": null,
"cdna_length": 6458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1319C>T",
"hgvs_p": "p.Thr440Met",
"transcript": "XM_047415767.1",
"protein_id": "XP_047271723.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 1089,
"cds_start": 1319,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 1837,
"cdna_end": null,
"cdna_length": 6761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1394C>T",
"hgvs_p": "p.Thr465Met",
"transcript": "XM_006714041.4",
"protein_id": "XP_006714104.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 832,
"cds_start": 1394,
"cds_end": null,
"cds_length": 2499,
"cdna_start": 1532,
"cdna_end": null,
"cdna_length": 2934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Thr453Met",
"transcript": "XM_017008281.2",
"protein_id": "XP_016863770.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 820,
"cds_start": 1358,
"cds_end": null,
"cds_length": 2463,
"cdna_start": 1870,
"cdna_end": null,
"cdna_length": 3272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"dbsnp": "rs143344944",
"frequency_reference_population": 0.00008860348,
"hom_count_reference_population": 0,
"allele_count_reference_population": 143,
"gnomad_exomes_af": 0.0000868845,
"gnomad_genomes_af": 0.00010511,
"gnomad_exomes_ac": 127,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.020513445138931274,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.118,
"revel_prediction": "Benign",
"alphamissense_score": 0.0729,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.898,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000257290.10",
"gene_symbol": "PDGFRA",
"hgnc_id": 8803,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.1319C>T",
"hgvs_p": "p.Thr440Met"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000507166.5",
"gene_symbol": "ENSG00000282278",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1018-2450C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Gastrointestinal stromal tumor,Hereditary cancer-predisposing syndrome,Ovarian cancer,PDGFRA-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1 B:2",
"phenotype_combined": "Gastrointestinal stromal tumor|Hereditary cancer-predisposing syndrome|not provided|PDGFRA-related disorder|Ovarian cancer",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}