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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: 7-55198724-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=55198724&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 55198724,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_005228.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2709T>C",
"hgvs_p": "p.Thr903Thr",
"transcript": "NM_005228.5",
"protein_id": "NP_005219.2",
"transcript_support_level": null,
"aa_start": 903,
"aa_end": null,
"aa_length": 1210,
"cds_start": 2709,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 2970,
"cdna_end": null,
"cdna_length": 9905,
"mane_select": "ENST00000275493.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2709T>C",
"hgvs_p": "p.Thr903Thr",
"transcript": "ENST00000275493.7",
"protein_id": "ENSP00000275493.2",
"transcript_support_level": 1,
"aa_start": 903,
"aa_end": null,
"aa_length": 1210,
"cds_start": 2709,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 2970,
"cdna_end": null,
"cdna_length": 9905,
"mane_select": "NM_005228.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2574T>C",
"hgvs_p": "p.Thr858Thr",
"transcript": "ENST00000455089.5",
"protein_id": "ENSP00000415559.1",
"transcript_support_level": 1,
"aa_start": 858,
"aa_end": null,
"aa_length": 1091,
"cds_start": 2574,
"cds_end": null,
"cds_length": 3276,
"cdna_start": 2831,
"cdna_end": null,
"cdna_length": 3844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2574T>C",
"hgvs_p": "p.Thr858Thr",
"transcript": "NM_001346899.2",
"protein_id": "NP_001333828.1",
"transcript_support_level": null,
"aa_start": 858,
"aa_end": null,
"aa_length": 1165,
"cds_start": 2574,
"cds_end": null,
"cds_length": 3498,
"cdna_start": 2835,
"cdna_end": null,
"cdna_length": 9770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2550T>C",
"hgvs_p": "p.Thr850Thr",
"transcript": "NM_001346900.2",
"protein_id": "NP_001333829.1",
"transcript_support_level": null,
"aa_start": 850,
"aa_end": null,
"aa_length": 1157,
"cds_start": 2550,
"cds_end": null,
"cds_length": 3474,
"cdna_start": 2741,
"cdna_end": null,
"cdna_length": 9676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2550T>C",
"hgvs_p": "p.Thr850Thr",
"transcript": "ENST00000450046.2",
"protein_id": "ENSP00000413354.2",
"transcript_support_level": 4,
"aa_start": 850,
"aa_end": null,
"aa_length": 1157,
"cds_start": 2550,
"cds_end": null,
"cds_length": 3474,
"cdna_start": 2857,
"cdna_end": null,
"cdna_length": 9700,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2709T>C",
"hgvs_p": "p.Thr903Thr",
"transcript": "NM_001346898.2",
"protein_id": "NP_001333827.1",
"transcript_support_level": null,
"aa_start": 903,
"aa_end": null,
"aa_length": 1136,
"cds_start": 2709,
"cds_end": null,
"cds_length": 3411,
"cdna_start": 2970,
"cdna_end": null,
"cdna_length": 3983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2574T>C",
"hgvs_p": "p.Thr858Thr",
"transcript": "NM_001346897.2",
"protein_id": "NP_001333826.1",
"transcript_support_level": null,
"aa_start": 858,
"aa_end": null,
"aa_length": 1091,
"cds_start": 2574,
"cds_end": null,
"cds_length": 3276,
"cdna_start": 2835,
"cdna_end": null,
"cdna_length": 3848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.1908T>C",
"hgvs_p": "p.Thr636Thr",
"transcript": "NM_001346941.2",
"protein_id": "NP_001333870.1",
"transcript_support_level": null,
"aa_start": 636,
"aa_end": null,
"aa_length": 943,
"cds_start": 1908,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 2169,
"cdna_end": null,
"cdna_length": 9104,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2550T>C",
"hgvs_p": "p.Thr850Thr",
"transcript": "XM_047419952.1",
"protein_id": "XP_047275908.1",
"transcript_support_level": null,
"aa_start": 850,
"aa_end": null,
"aa_length": 1157,
"cds_start": 2550,
"cds_end": null,
"cds_length": 3474,
"cdna_start": 41519,
"cdna_end": null,
"cdna_length": 48454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.2550T>C",
"hgvs_p": "p.Thr850Thr",
"transcript": "XM_047419953.1",
"protein_id": "XP_047275909.1",
"transcript_support_level": null,
"aa_start": 850,
"aa_end": null,
"aa_length": 1157,
"cds_start": 2550,
"cds_end": null,
"cds_length": 3474,
"cdna_start": 3696,
"cdna_end": null,
"cdna_length": 10631,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "n.39T>C",
"hgvs_p": null,
"transcript": "ENST00000485503.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 665,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "n.453T>C",
"hgvs_p": null,
"transcript": "ENST00000700146.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"hgvs_c": "c.898-6623T>C",
"hgvs_p": null,
"transcript": "ENST00000700145.1",
"protein_id": "ENSP00000514824.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 343,
"cds_start": -4,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EGFR-AS1",
"gene_hgnc_id": 40207,
"hgvs_c": "n.207+14039A>G",
"hgvs_p": null,
"transcript": "ENST00000836806.1",
"protein_id": null,
"transcript_support_level": null,
"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": 986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EGFR",
"gene_hgnc_id": 3236,
"dbsnp": "rs1140475",
"frequency_reference_population": 0.8806037,
"hom_count_reference_population": 626480,
"allele_count_reference_population": 1421393,
"gnomad_exomes_af": 0.878939,
"gnomad_genomes_af": 0.896585,
"gnomad_exomes_ac": 1284879,
"gnomad_genomes_ac": 136514,
"gnomad_exomes_homalt": 565211,
"gnomad_genomes_homalt": 61269,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8999999761581421,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.9,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.099,
"phylop100way_prediction": "Benign",
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_005228.5",
"gene_symbol": "EGFR",
"hgnc_id": 3236,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2709T>C",
"hgvs_p": "p.Thr903Thr"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000836806.1",
"gene_symbol": "EGFR-AS1",
"hgnc_id": 40207,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.207+14039A>G",
"hgvs_p": null
}
],
"clinvar_disease": " 2, neonatal,EGFR-related lung cancer,Inflammatory skin and bowel disease,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "EGFR-related lung cancer|Inflammatory skin and bowel disease, neonatal, 2|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}