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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: 7-116740034-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=116740034&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 116740034,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000397752.8",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1477G>C",
"hgvs_p": "p.Glu493Gln",
"transcript": "NM_000245.4",
"protein_id": "NP_000236.2",
"transcript_support_level": null,
"aa_start": 493,
"aa_end": null,
"aa_length": 1390,
"cds_start": 1477,
"cds_end": null,
"cds_length": 4173,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 6822,
"mane_select": "ENST00000397752.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1477G>C",
"hgvs_p": "p.Glu493Gln",
"transcript": "ENST00000397752.8",
"protein_id": "ENSP00000380860.3",
"transcript_support_level": 1,
"aa_start": 493,
"aa_end": null,
"aa_length": 1390,
"cds_start": 1477,
"cds_end": null,
"cds_length": 4173,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 6822,
"mane_select": "NM_000245.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1477G>C",
"hgvs_p": "p.Glu493Gln",
"transcript": "ENST00000318493.11",
"protein_id": "ENSP00000317272.6",
"transcript_support_level": 1,
"aa_start": 493,
"aa_end": null,
"aa_length": 1408,
"cds_start": 1477,
"cds_end": null,
"cds_length": 4227,
"cdna_start": 1873,
"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": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.1477G>C",
"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": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1477G>C",
"hgvs_p": "p.Glu493Gln",
"transcript": "NM_001127500.3",
"protein_id": "NP_001120972.1",
"transcript_support_level": null,
"aa_start": 493,
"aa_end": null,
"aa_length": 1408,
"cds_start": 1477,
"cds_end": null,
"cds_length": 4227,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 6876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.187G>C",
"hgvs_p": "p.Glu63Gln",
"transcript": "NM_001324402.2",
"protein_id": "NP_001311331.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 960,
"cds_start": 187,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 659,
"cdna_end": null,
"cdna_length": 5608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1477G>C",
"hgvs_p": "p.Glu493Gln",
"transcript": "NM_001324401.3",
"protein_id": "NP_001311330.1",
"transcript_support_level": null,
"aa_start": 493,
"aa_end": null,
"aa_length": 934,
"cds_start": 1477,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 3215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1477G>C",
"hgvs_p": "p.Glu493Gln",
"transcript": "ENST00000422097.2",
"protein_id": "ENSP00000398776.2",
"transcript_support_level": 3,
"aa_start": 493,
"aa_end": null,
"aa_length": 934,
"cds_start": 1477,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1534G>C",
"hgvs_p": "p.Glu512Gln",
"transcript": "XM_011516223.2",
"protein_id": "XP_011514525.1",
"transcript_support_level": null,
"aa_start": 512,
"aa_end": null,
"aa_length": 1409,
"cds_start": 1534,
"cds_end": null,
"cds_length": 4230,
"cdna_start": 1923,
"cdna_end": null,
"cdna_length": 6872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.1534G>C",
"hgvs_p": "p.Glu512Gln",
"transcript": "XM_047420400.1",
"protein_id": "XP_047276356.1",
"transcript_support_level": null,
"aa_start": 512,
"aa_end": null,
"aa_length": 783,
"cds_start": 1534,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 1923,
"cdna_end": null,
"cdna_length": 2929,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.457G>C",
"hgvs_p": null,
"transcript": "ENST00000495962.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"dbsnp": "rs965319455",
"frequency_reference_population": 0.000014249321,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.0000143654,
"gnomad_genomes_af": 0.0000131347,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08231151103973389,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.106,
"revel_prediction": "Benign",
"alphamissense_score": 0.0802,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.62,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000397752.8",
"gene_symbol": "MET",
"hgnc_id": 7029,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.1477G>C",
"hgvs_p": "p.Glu493Gln"
}
],
"clinvar_disease": " IIa 11, distal,Arthrogryposis,Autosomal recessive nonsyndromic hearing loss 97,Hepatocellular carcinoma,Hereditary cancer-predisposing syndrome,MET-related disorder,Osteofibrous dysplasia,Papillary renal cell carcinoma type 1,Renal cell carcinoma,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:8",
"phenotype_combined": "Renal cell carcinoma|not provided|Hereditary cancer-predisposing syndrome|Autosomal recessive nonsyndromic hearing loss 97|MET-related disorder|Osteofibrous dysplasia;Arthrogryposis, distal, IIa 11;Autosomal recessive nonsyndromic hearing loss 97;Papillary renal cell carcinoma type 1;Hepatocellular carcinoma",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}