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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: 2-48963475-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=48963475&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 48963475,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000406846.7",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSHR",
"gene_hgnc_id": 3969,
"hgvs_c": "c.1346C>A",
"hgvs_p": "p.Thr449Asn",
"transcript": "NM_000145.4",
"protein_id": "NP_000136.2",
"transcript_support_level": null,
"aa_start": 449,
"aa_end": null,
"aa_length": 695,
"cds_start": 1346,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1444,
"cdna_end": null,
"cdna_length": 2762,
"mane_select": "ENST00000406846.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSHR",
"gene_hgnc_id": 3969,
"hgvs_c": "c.1346C>A",
"hgvs_p": "p.Thr449Asn",
"transcript": "ENST00000406846.7",
"protein_id": "ENSP00000384708.2",
"transcript_support_level": 1,
"aa_start": 449,
"aa_end": null,
"aa_length": 695,
"cds_start": 1346,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1444,
"cdna_end": null,
"cdna_length": 2762,
"mane_select": "NM_000145.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSHR",
"gene_hgnc_id": 3969,
"hgvs_c": "c.1268C>A",
"hgvs_p": "p.Thr423Asn",
"transcript": "ENST00000304421.8",
"protein_id": "ENSP00000306780.4",
"transcript_support_level": 1,
"aa_start": 423,
"aa_end": null,
"aa_length": 669,
"cds_start": 1268,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 1332,
"cdna_end": null,
"cdna_length": 2176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSHR",
"gene_hgnc_id": 3969,
"hgvs_c": "c.1268C>A",
"hgvs_p": "p.Thr423Asn",
"transcript": "NM_181446.3",
"protein_id": "NP_852111.2",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 669,
"cds_start": 1268,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 1366,
"cdna_end": null,
"cdna_length": 2684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSHR",
"gene_hgnc_id": 3969,
"hgvs_c": "c.1448C>A",
"hgvs_p": "p.Thr483Asn",
"transcript": "XM_011532733.3",
"protein_id": "XP_011531035.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 729,
"cds_start": 1448,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 1546,
"cdna_end": null,
"cdna_length": 2864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSHR",
"gene_hgnc_id": 3969,
"hgvs_c": "c.1115C>A",
"hgvs_p": "p.Thr372Asn",
"transcript": "XM_047443867.1",
"protein_id": "XP_047299823.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 618,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1857,
"cdna_start": 1400,
"cdna_end": null,
"cdna_length": 2718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSHR",
"gene_hgnc_id": 3969,
"hgvs_c": "c.554C>A",
"hgvs_p": "p.Thr185Asn",
"transcript": "XM_011532735.3",
"protein_id": "XP_011531037.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 431,
"cds_start": 554,
"cds_end": null,
"cds_length": 1296,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 2457,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000282890",
"gene_hgnc_id": 58158,
"hgvs_c": "n.492+17070G>T",
"hgvs_p": null,
"transcript": "ENST00000634588.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 2698,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FSHR",
"gene_hgnc_id": 3969,
"dbsnp": "rs28928870",
"frequency_reference_population": 0.0000013681444,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136814,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9191375374794006,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.701,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2536,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"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": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PM5",
"PP2",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000406846.7",
"gene_symbol": "FSHR",
"hgnc_id": 3969,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1346C>A",
"hgvs_p": "p.Thr449Asn"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000634588.1",
"gene_symbol": "ENSG00000282890",
"hgnc_id": 58158,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.492+17070G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}