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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: 2-162173207-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=162173207&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 162173207,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004460.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.2049G>A",
"hgvs_p": "p.Met683Ile",
"transcript": "NM_004460.5",
"protein_id": "NP_004451.2",
"transcript_support_level": null,
"aa_start": 683,
"aa_end": null,
"aa_length": 760,
"cds_start": 2049,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000188790.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004460.5"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.2049G>A",
"hgvs_p": "p.Met683Ile",
"transcript": "ENST00000188790.9",
"protein_id": "ENSP00000188790.4",
"transcript_support_level": 1,
"aa_start": 683,
"aa_end": null,
"aa_length": 760,
"cds_start": 2049,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004460.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000188790.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "n.*930G>A",
"hgvs_p": null,
"transcript": "ENST00000422436.5",
"protein_id": "ENSP00000417028.1",
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000422436.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "n.*930G>A",
"hgvs_p": null,
"transcript": "ENST00000422436.5",
"protein_id": "ENSP00000417028.1",
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000422436.5"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.2034G>A",
"hgvs_p": "p.Met678Ile",
"transcript": "ENST00000856821.1",
"protein_id": "ENSP00000526880.1",
"transcript_support_level": null,
"aa_start": 678,
"aa_end": null,
"aa_length": 755,
"cds_start": 2034,
"cds_end": null,
"cds_length": 2268,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856821.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.2025G>A",
"hgvs_p": "p.Met675Ile",
"transcript": "ENST00000856822.1",
"protein_id": "ENSP00000526881.1",
"transcript_support_level": null,
"aa_start": 675,
"aa_end": null,
"aa_length": 752,
"cds_start": 2025,
"cds_end": null,
"cds_length": 2259,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856822.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.2004G>A",
"hgvs_p": "p.Met668Ile",
"transcript": "ENST00000856823.1",
"protein_id": "ENSP00000526882.1",
"transcript_support_level": null,
"aa_start": 668,
"aa_end": null,
"aa_length": 745,
"cds_start": 2004,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856823.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.1974G>A",
"hgvs_p": "p.Met658Ile",
"transcript": "NM_001291807.3",
"protein_id": "NP_001278736.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 735,
"cds_start": 1974,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291807.3"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.1974G>A",
"hgvs_p": "p.Met658Ile",
"transcript": "ENST00000443424.5",
"protein_id": "ENSP00000411391.1",
"transcript_support_level": 2,
"aa_start": 658,
"aa_end": null,
"aa_length": 735,
"cds_start": 1974,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000443424.5"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.1884G>A",
"hgvs_p": "p.Met628Ile",
"transcript": "ENST00000963584.1",
"protein_id": "ENSP00000633643.1",
"transcript_support_level": null,
"aa_start": 628,
"aa_end": null,
"aa_length": 705,
"cds_start": 1884,
"cds_end": null,
"cds_length": 2118,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963584.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.1737G>A",
"hgvs_p": "p.Met579Ile",
"transcript": "ENST00000963585.1",
"protein_id": "ENSP00000633644.1",
"transcript_support_level": null,
"aa_start": 579,
"aa_end": null,
"aa_length": 656,
"cds_start": 1737,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963585.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "c.2019G>A",
"hgvs_p": "p.Met673Ile",
"transcript": "XM_011510796.4",
"protein_id": "XP_011509098.1",
"transcript_support_level": null,
"aa_start": 673,
"aa_end": null,
"aa_length": 750,
"cds_start": 2019,
"cds_end": null,
"cds_length": 2253,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510796.4"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236841",
"gene_hgnc_id": null,
"hgvs_c": "n.4110C>T",
"hgvs_p": null,
"transcript": "ENST00000418968.5",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000418968.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "n.350G>A",
"hgvs_p": null,
"transcript": "ENST00000461506.1",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000461506.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "n.72G>A",
"hgvs_p": null,
"transcript": "ENST00000462608.5",
"protein_id": "ENSP00000441940.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000462608.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"hgvs_c": "n.1883G>A",
"hgvs_p": null,
"transcript": "ENST00000480044.5",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000480044.5"
}
],
"gene_symbol": "FAP",
"gene_hgnc_id": 3590,
"dbsnp": "rs749983039",
"frequency_reference_population": 0.000016121552,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000157462,
"gnomad_genomes_af": 0.0000197262,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.621070384979248,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.236,
"revel_prediction": "Benign",
"alphamissense_score": 0.5111,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.951,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004460.5",
"gene_symbol": "FAP",
"hgnc_id": 3590,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2049G>A",
"hgvs_p": "p.Met683Ile"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000418968.5",
"gene_symbol": "ENSG00000236841",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.4110C>T",
"hgvs_p": null
}
],
"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
}