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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: 4-54273621-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=54273621&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 17,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "PDGFRA",
"hgnc_id": 8803,
"hgvs_c": "c.1524C>T",
"hgvs_p": "p.Thr508Thr",
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 0,
"score": -17,
"transcript": "NM_001347828.2",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000282278",
"hgnc_id": null,
"hgvs_c": "c.1018-1304C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -10,
"transcript": "ENST00000507166.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_score": -17,
"allele_count_reference_population": 34,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.8,
"chr": "4",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Gastrointestinal stromal tumor,Hereditary cancer-predisposing syndrome,PDGFRA-related disorder",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.800000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6378,
"cdna_start": 1584,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_006206.6",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000257290.10",
"protein_coding": true,
"protein_id": "NP_006197.1",
"strand": true,
"transcript": "NM_006206.6",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6378,
"cdna_start": 1584,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000257290.10",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006206.6",
"protein_coding": true,
"protein_id": "ENSP00000257290.5",
"strand": true,
"transcript": "ENST00000257290.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 849,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2550,
"cdna_start": null,
"cds_end": null,
"cds_length": 2550,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000507166.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000282278",
"hgvs_c": "c.1018-1304C>T",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423325.1",
"strand": true,
"transcript": "ENST00000507166.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2417,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000509092.5",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "n.1267C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000509092.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2991,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000509490.5",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "n.1449C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000424218.1",
"strand": true,
"transcript": "ENST00000509490.5",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1114,
"aa_ref": "T",
"aa_start": 508,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6456,
"cdna_start": 1662,
"cds_end": null,
"cds_length": 3345,
"cds_start": 1524,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001347828.2",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1524C>T",
"hgvs_p": "p.Thr508Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001334757.1",
"strand": true,
"transcript": "NM_001347828.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1102,
"aa_ref": "T",
"aa_start": 496,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6794,
"cdna_start": 2000,
"cds_end": null,
"cds_length": 3309,
"cds_start": 1488,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001347830.2",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1488C>T",
"hgvs_p": "p.Thr496Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001334759.1",
"strand": true,
"transcript": "NM_001347830.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6599,
"cdna_start": 1805,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001347829.2",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001334758.1",
"strand": true,
"transcript": "NM_001347829.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6448,
"cdna_start": 1654,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000870889.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540948.1",
"strand": true,
"transcript": "ENST00000870889.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6627,
"cdna_start": 1834,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000870890.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540949.1",
"strand": true,
"transcript": "ENST00000870890.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6778,
"cdna_start": 1986,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000958745.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628804.1",
"strand": true,
"transcript": "ENST00000958745.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6988,
"cdna_start": 2195,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000958746.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628805.1",
"strand": true,
"transcript": "ENST00000958746.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6448,
"cdna_start": 1653,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000958749.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628808.1",
"strand": true,
"transcript": "ENST00000958749.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
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"aa_length": 1089,
"aa_ref": "T",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6341,
"cdna_start": 1547,
"cds_end": null,
"cds_length": 3270,
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"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
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"feature": "ENST00000958750.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628809.1",
"strand": true,
"transcript": "ENST00000958750.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6523,
"cdna_start": 1730,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000958751.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628810.1",
"strand": true,
"transcript": "ENST00000958751.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6370,
"cdna_start": 1579,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000958752.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628811.1",
"strand": true,
"transcript": "ENST00000958752.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
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"aa_length": 1089,
"aa_ref": "T",
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 6000,
"cdna_start": 2106,
"cds_end": null,
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"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000958753.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000628812.1",
"strand": true,
"transcript": "ENST00000958753.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1089,
"aa_ref": "T",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8031,
"cdna_start": 3238,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000958754.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628813.1",
"strand": true,
"transcript": "ENST00000958754.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
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"aa_length": 1089,
"aa_ref": "T",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7203,
"cdna_start": 2408,
"cds_end": null,
"cds_length": 3270,
"cds_start": 1449,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000958755.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1449C>T",
"hgvs_p": "p.Thr483Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628814.1",
"strand": true,
"transcript": "ENST00000958755.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1087,
"aa_ref": "T",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6381,
"cdna_start": 1590,
"cds_end": null,
"cds_length": 3264,
"cds_start": 1443,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000958748.1",
"gene_hgnc_id": 8803,
"gene_symbol": "PDGFRA",
"hgvs_c": "c.1443C>T",
"hgvs_p": "p.Thr481Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628807.1",
"strand": true,
"transcript": "ENST00000958748.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
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