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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: 6-41158917-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=41158917&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 41158917,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000373113.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREM2",
"gene_hgnc_id": 17761,
"hgvs_c": "c.632T>C",
"hgvs_p": "p.Leu211Pro",
"transcript": "NM_018965.4",
"protein_id": "NP_061838.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 230,
"cds_start": 632,
"cds_end": null,
"cds_length": 693,
"cdna_start": 666,
"cdna_end": null,
"cdna_length": 983,
"mane_select": "ENST00000373113.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREM2",
"gene_hgnc_id": 17761,
"hgvs_c": "c.632T>C",
"hgvs_p": "p.Leu211Pro",
"transcript": "ENST00000373113.8",
"protein_id": "ENSP00000362205.3",
"transcript_support_level": 1,
"aa_start": 211,
"aa_end": null,
"aa_length": 230,
"cds_start": 632,
"cds_end": null,
"cds_length": 693,
"cdna_start": 666,
"cdna_end": null,
"cdna_length": 983,
"mane_select": "NM_018965.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TREM2",
"gene_hgnc_id": 17761,
"hgvs_c": "c.*3T>C",
"hgvs_p": null,
"transcript": "ENST00000373122.8",
"protein_id": "ENSP00000362214.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 222,
"cds_start": -4,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1012,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TREM2",
"gene_hgnc_id": 17761,
"hgvs_c": "c.483-137T>C",
"hgvs_p": null,
"transcript": "ENST00000338469.3",
"protein_id": "ENSP00000342651.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": -4,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TREM2",
"gene_hgnc_id": 17761,
"hgvs_c": "c.483-137T>C",
"hgvs_p": null,
"transcript": "NM_001271821.2",
"protein_id": "NP_001258750.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": -4,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000290034",
"gene_hgnc_id": null,
"hgvs_c": "n.364+3354A>G",
"hgvs_p": null,
"transcript": "ENST00000702590.2",
"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": 1339,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000290034",
"gene_hgnc_id": null,
"hgvs_c": "n.364+3354A>G",
"hgvs_p": null,
"transcript": "ENST00000736037.1",
"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": 1329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000290034",
"gene_hgnc_id": null,
"hgvs_c": "n.362+3356A>G",
"hgvs_p": null,
"transcript": "ENST00000736038.1",
"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": 1333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TREM2",
"gene_hgnc_id": 17761,
"dbsnp": "rs2234256",
"frequency_reference_population": 0.010917215,
"hom_count_reference_population": 854,
"allele_count_reference_population": 17622,
"gnomad_exomes_af": 0.00803276,
"gnomad_genomes_af": 0.0386116,
"gnomad_exomes_ac": 11743,
"gnomad_genomes_ac": 5879,
"gnomad_exomes_homalt": 515,
"gnomad_genomes_homalt": 339,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0014629364013671875,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.012,
"revel_prediction": "Benign",
"alphamissense_score": 0.0448,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.328,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000373113.8",
"gene_symbol": "TREM2",
"hgnc_id": 17761,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.632T>C",
"hgvs_p": "p.Leu211Pro"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000702590.2",
"gene_symbol": "ENSG00000290034",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.364+3354A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy 1,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"phenotype_combined": "Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy 1|not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}