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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: 2-162188338-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=162188338&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "FAP",
"hgnc_id": 3590,
"hgvs_c": "c.1645G>C",
"hgvs_p": "p.Val549Leu",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_004460.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.847,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.06,
"chr": "2",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8699543476104736,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 760,
"aa_ref": "V",
"aa_start": 549,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2696,
"cdna_start": 1763,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1645,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_004460.5",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1645G>C",
"hgvs_p": "p.Val549Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000188790.9",
"protein_coding": true,
"protein_id": "NP_004451.2",
"strand": false,
"transcript": "NM_004460.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 760,
"aa_ref": "V",
"aa_start": 549,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2696,
"cdna_start": 1763,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1645,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000188790.9",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1645G>C",
"hgvs_p": "p.Val549Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004460.5",
"protein_coding": true,
"protein_id": "ENSP00000188790.4",
"strand": false,
"transcript": "ENST00000188790.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1537,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000422436.5",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "n.*526G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000417028.1",
"strand": false,
"transcript": "ENST00000422436.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1537,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000422436.5",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "n.*526G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000417028.1",
"strand": false,
"transcript": "ENST00000422436.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 755,
"aa_ref": "V",
"aa_start": 549,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2719,
"cdna_start": 1804,
"cds_end": null,
"cds_length": 2268,
"cds_start": 1645,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000856821.1",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1645G>C",
"hgvs_p": "p.Val549Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526880.1",
"strand": false,
"transcript": "ENST00000856821.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 752,
"aa_ref": "V",
"aa_start": 541,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2691,
"cdna_start": 1758,
"cds_end": null,
"cds_length": 2259,
"cds_start": 1621,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000856822.1",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1621G>C",
"hgvs_p": "p.Val541Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526881.1",
"strand": false,
"transcript": "ENST00000856822.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 745,
"aa_ref": "V",
"aa_start": 534,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2622,
"cdna_start": 1691,
"cds_end": null,
"cds_length": 2238,
"cds_start": 1600,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000856823.1",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1600G>C",
"hgvs_p": "p.Val534Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526882.1",
"strand": false,
"transcript": "ENST00000856823.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 735,
"aa_ref": "V",
"aa_start": 524,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2621,
"cdna_start": 1688,
"cds_end": null,
"cds_length": 2208,
"cds_start": 1570,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_001291807.3",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1570G>C",
"hgvs_p": "p.Val524Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278736.1",
"strand": false,
"transcript": "NM_001291807.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 735,
"aa_ref": "V",
"aa_start": 524,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2598,
"cdna_start": 1699,
"cds_end": null,
"cds_length": 2208,
"cds_start": 1570,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000443424.5",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1570G>C",
"hgvs_p": "p.Val524Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000411391.1",
"strand": false,
"transcript": "ENST00000443424.5",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 705,
"aa_ref": "V",
"aa_start": 549,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2490,
"cdna_start": 1723,
"cds_end": null,
"cds_length": 2118,
"cds_start": 1645,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000963584.1",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1645G>C",
"hgvs_p": "p.Val549Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633643.1",
"strand": false,
"transcript": "ENST00000963584.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 750,
"aa_ref": "V",
"aa_start": 539,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2866,
"cdna_start": 1933,
"cds_end": null,
"cds_length": 2253,
"cds_start": 1615,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_011510796.4",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1615G>C",
"hgvs_p": "p.Val539Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011509098.1",
"strand": false,
"transcript": "XM_011510796.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 656,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2339,
"cdna_start": null,
"cds_end": null,
"cds_length": 1971,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000963585.1",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "c.1451-118G>C",
"hgvs_p": null,
"intron_rank": 17,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633644.1",
"strand": false,
"transcript": "ENST00000963585.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 698,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000497414.1",
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"hgvs_c": "n.532G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000497414.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs771148895",
"effect": "missense_variant",
"frequency_reference_population": 6.844805e-7,
"gene_hgnc_id": 3590,
"gene_symbol": "FAP",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.8448e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.498,
"pos": 162188338,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.435,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_004460.5"
}
]
}