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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: 11-60064262-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=60064262&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 60064262,
"ref": "T",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_006138.5",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.295T>C",
"hgvs_p": "p.Phe99Leu",
"transcript": "NM_006138.5",
"protein_id": "NP_006129.4",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 214,
"cds_start": 295,
"cds_end": null,
"cds_length": 645,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 1618,
"mane_select": "ENST00000278865.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006138.5"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.295T>C",
"hgvs_p": "p.Phe99Leu",
"transcript": "ENST00000278865.8",
"protein_id": "ENSP00000278865.3",
"transcript_support_level": 1,
"aa_start": 99,
"aa_end": null,
"aa_length": 214,
"cds_start": 295,
"cds_end": null,
"cds_length": 645,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 1618,
"mane_select": "NM_006138.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000278865.8"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.157T>C",
"hgvs_p": "p.Phe53Leu",
"transcript": "NM_001031809.2",
"protein_id": "NP_001026979.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 168,
"cds_start": 157,
"cds_end": null,
"cds_length": 507,
"cdna_start": 248,
"cdna_end": null,
"cdna_length": 1480,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001031809.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.157T>C",
"hgvs_p": "p.Phe53Leu",
"transcript": "ENST00000358152.6",
"protein_id": "ENSP00000350872.2",
"transcript_support_level": 5,
"aa_start": 53,
"aa_end": null,
"aa_length": 168,
"cds_start": 157,
"cds_end": null,
"cds_length": 507,
"cdna_start": 285,
"cdna_end": null,
"cdna_length": 1516,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358152.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.-75T>C",
"hgvs_p": null,
"transcript": "NM_001031666.2",
"protein_id": "NP_001026836.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 91,
"cds_start": null,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1309,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001031666.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.-75T>C",
"hgvs_p": null,
"transcript": "ENST00000395032.6",
"protein_id": "ENSP00000378473.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 91,
"cds_start": null,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 867,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395032.6"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.115T>C",
"hgvs_p": "p.Phe39Leu",
"transcript": "XM_011545363.4",
"protein_id": "XP_011543665.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 154,
"cds_start": 115,
"cds_end": null,
"cds_length": 465,
"cdna_start": 171,
"cdna_end": null,
"cdna_length": 1403,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011545363.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.-75T>C",
"hgvs_p": null,
"transcript": "NM_001031666.2",
"protein_id": "NP_001026836.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 91,
"cds_start": null,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1309,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001031666.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "c.-75T>C",
"hgvs_p": null,
"transcript": "ENST00000395032.6",
"protein_id": "ENSP00000378473.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 91,
"cds_start": null,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 867,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395032.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"hgvs_c": "n.222T>C",
"hgvs_p": null,
"transcript": "ENST00000525686.1",
"protein_id": "ENSP00000434109.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 746,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000525686.1"
}
],
"gene_symbol": "MS4A3",
"gene_hgnc_id": 7317,
"dbsnp": "rs762015062",
"frequency_reference_population": 0.00000498235,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000481579,
"gnomad_genomes_af": 0.00000657393,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9313968420028687,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.2879999876022339,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.19,
"revel_prediction": "Benign",
"alphamissense_score": 0.95,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.61,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0489778149598174,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006138.5",
"gene_symbol": "MS4A3",
"hgnc_id": 7317,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.295T>C",
"hgvs_p": "p.Phe99Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}