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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: 7-116699985-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=116699985&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 116699985,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000397752.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Thr301Ala",
"transcript": "NM_000245.4",
"protein_id": "NP_000236.2",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 1390,
"cds_start": 901,
"cds_end": null,
"cds_length": 4173,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 6822,
"mane_select": "ENST00000397752.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Thr301Ala",
"transcript": "ENST00000397752.8",
"protein_id": "ENSP00000380860.3",
"transcript_support_level": 1,
"aa_start": 301,
"aa_end": null,
"aa_length": 1390,
"cds_start": 901,
"cds_end": null,
"cds_length": 4173,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 6822,
"mane_select": "NM_000245.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Thr301Ala",
"transcript": "ENST00000318493.11",
"protein_id": "ENSP00000317272.6",
"transcript_support_level": 1,
"aa_start": 301,
"aa_end": null,
"aa_length": 1408,
"cds_start": 901,
"cds_end": null,
"cds_length": 4227,
"cdna_start": 1297,
"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": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "n.901A>G",
"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": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Thr301Ala",
"transcript": "NM_001127500.3",
"protein_id": "NP_001120972.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 1408,
"cds_start": 901,
"cds_end": null,
"cds_length": 4227,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 6876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Thr301Ala",
"transcript": "NM_001324401.3",
"protein_id": "NP_001311330.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 934,
"cds_start": 901,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 3215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Thr301Ala",
"transcript": "ENST00000422097.2",
"protein_id": "ENSP00000398776.2",
"transcript_support_level": 3,
"aa_start": 301,
"aa_end": null,
"aa_length": 934,
"cds_start": 901,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.958A>G",
"hgvs_p": "p.Thr320Ala",
"transcript": "XM_011516223.2",
"protein_id": "XP_011514525.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 1409,
"cds_start": 958,
"cds_end": null,
"cds_length": 4230,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 6872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.958A>G",
"hgvs_p": "p.Thr320Ala",
"transcript": "XM_047420400.1",
"protein_id": "XP_047276356.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 783,
"cds_start": 958,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 1347,
"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": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"hgvs_c": "c.-91+27408A>G",
"hgvs_p": null,
"transcript": "NM_001324402.2",
"protein_id": "NP_001311331.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 960,
"cds_start": -4,
"cds_end": null,
"cds_length": 2883,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5608,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COMETT",
"gene_hgnc_id": 51196,
"hgvs_c": "n.98+24413T>C",
"hgvs_p": null,
"transcript": "ENST00000450063.2",
"protein_id": null,
"transcript_support_level": 2,
"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": 1018,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COMETT",
"gene_hgnc_id": 51196,
"hgvs_c": "n.98+24413T>C",
"hgvs_p": null,
"transcript": "ENST00000757593.1",
"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": 694,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COMETT",
"gene_hgnc_id": 51196,
"hgvs_c": "n.98+24413T>C",
"hgvs_p": null,
"transcript": "ENST00000757594.1",
"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": 989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MET",
"gene_hgnc_id": 7029,
"dbsnp": "rs201687037",
"frequency_reference_population": 0.0005675179,
"hom_count_reference_population": 1,
"allele_count_reference_population": 916,
"gnomad_exomes_af": 0.000589704,
"gnomad_genomes_af": 0.000354573,
"gnomad_exomes_ac": 862,
"gnomad_genomes_ac": 54,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10883194208145142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.243,
"revel_prediction": "Benign",
"alphamissense_score": 0.1523,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.625,
"phylop100way_prediction": "Uncertain_significance",
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000397752.8",
"gene_symbol": "MET",
"hgnc_id": 7029,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Thr301Ala"
},
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000450063.2",
"gene_symbol": "COMETT",
"hgnc_id": 51196,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.98+24413T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 97,Hereditary cancer-predisposing syndrome,Hereditary papillary renal cell carcinoma,Papillary renal cell carcinoma type 1,Renal cell carcinoma,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:7 LB:3 O:1",
"phenotype_combined": "not provided|Hereditary cancer-predisposing syndrome|Renal cell carcinoma|Autosomal recessive nonsyndromic hearing loss 97|not specified|Papillary renal cell carcinoma type 1|Hereditary papillary renal cell carcinoma",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}