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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: 7-116771521-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=116771521&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 116771521,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000397752.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.2754C>A",
"hgvs_p": "p.Thr918Thr",
"transcript": "NM_000245.4",
"protein_id": "NP_000236.2",
"transcript_support_level": null,
"aa_start": 918,
"aa_end": null,
"aa_length": 1390,
"cds_start": 2754,
"cds_end": null,
"cds_length": 4173,
"cdna_start": 3150,
"cdna_end": null,
"cdna_length": 6822,
"mane_select": "ENST00000397752.8",
"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": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.2754C>A",
"hgvs_p": "p.Thr918Thr",
"transcript": "ENST00000397752.8",
"protein_id": "ENSP00000380860.3",
"transcript_support_level": 1,
"aa_start": 918,
"aa_end": null,
"aa_length": 1390,
"cds_start": 2754,
"cds_end": null,
"cds_length": 4173,
"cdna_start": 3150,
"cdna_end": null,
"cdna_length": 6822,
"mane_select": "NM_000245.4",
"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": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.2808C>A",
"hgvs_p": "p.Thr936Thr",
"transcript": "ENST00000318493.11",
"protein_id": "ENSP00000317272.6",
"transcript_support_level": 1,
"aa_start": 936,
"aa_end": null,
"aa_length": 1408,
"cds_start": 2808,
"cds_end": null,
"cds_length": 4227,
"cdna_start": 3204,
"cdna_end": null,
"cdna_length": 6876,
"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": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.*359C>A",
"hgvs_p": null,
"transcript": "ENST00000436117.3",
"protein_id": "ENSP00000410980.2",
"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": 6722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.*359C>A",
"hgvs_p": null,
"transcript": "ENST00000436117.3",
"protein_id": "ENSP00000410980.2",
"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": 6722,
"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": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.2808C>A",
"hgvs_p": "p.Thr936Thr",
"transcript": "NM_001127500.3",
"protein_id": "NP_001120972.1",
"transcript_support_level": null,
"aa_start": 936,
"aa_end": null,
"aa_length": 1408,
"cds_start": 2808,
"cds_end": null,
"cds_length": 4227,
"cdna_start": 3204,
"cdna_end": null,
"cdna_length": 6876,
"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": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1464C>A",
"hgvs_p": "p.Thr488Thr",
"transcript": "NM_001324402.2",
"protein_id": "NP_001311331.1",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 960,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 1936,
"cdna_end": null,
"cdna_length": 5608,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.150C>A",
"hgvs_p": "p.Thr50Thr",
"transcript": "ENST00000454623.1",
"protein_id": "ENSP00000398140.1",
"transcript_support_level": 5,
"aa_start": 50,
"aa_end": null,
"aa_length": 157,
"cds_start": 150,
"cds_end": null,
"cds_length": 475,
"cdna_start": 150,
"cdna_end": null,
"cdna_length": 475,
"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": 14,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.2811C>A",
"hgvs_p": "p.Thr937Thr",
"transcript": "XM_011516223.2",
"protein_id": "XP_011514525.1",
"transcript_support_level": null,
"aa_start": 937,
"aa_end": null,
"aa_length": 1409,
"cds_start": 2811,
"cds_end": null,
"cds_length": 4230,
"cdna_start": 3200,
"cdna_end": null,
"cdna_length": 6872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"dbsnp": "rs770886012",
"frequency_reference_population": 0.000028053792,
"hom_count_reference_population": 0,
"allele_count_reference_population": 41,
"gnomad_exomes_af": 0.0000280538,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 41,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.339,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000397752.8",
"gene_symbol": "MET",
"hgnc_id": 7029,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.2754C>A",
"hgvs_p": "p.Thr918Thr"
}
],
"clinvar_disease": "Hereditary cancer-predisposing syndrome,Papillary renal cell carcinoma type 1,Renal cell carcinoma",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Renal cell carcinoma|Hereditary cancer-predisposing syndrome|Papillary renal cell carcinoma type 1",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}