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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: 2-127701707-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=127701707&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 127701707,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_032740.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFT2D3",
"gene_hgnc_id": 28767,
"hgvs_c": "c.179C>A",
"hgvs_p": "p.Ser60*",
"transcript": "NM_032740.4",
"protein_id": "NP_116129.3",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 215,
"cds_start": 179,
"cds_end": null,
"cds_length": 648,
"cdna_start": 211,
"cdna_end": null,
"cdna_length": 3746,
"mane_select": "ENST00000310981.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SFT2D3",
"gene_hgnc_id": 28767,
"hgvs_c": "c.179C>A",
"hgvs_p": "p.Ser60*",
"transcript": "ENST00000310981.6",
"protein_id": "ENSP00000310803.3",
"transcript_support_level": 6,
"aa_start": 60,
"aa_end": null,
"aa_length": 215,
"cds_start": 179,
"cds_end": null,
"cds_length": 648,
"cdna_start": 211,
"cdna_end": null,
"cdna_length": 3746,
"mane_select": "NM_032740.4",
"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": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR33",
"gene_hgnc_id": 25651,
"hgvs_c": "c.*4616G>T",
"hgvs_p": null,
"transcript": "NM_018383.5",
"protein_id": "NP_060853.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1336,
"cds_start": -4,
"cds_end": null,
"cds_length": 4011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9490,
"mane_select": "ENST00000322313.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR33",
"gene_hgnc_id": 25651,
"hgvs_c": "c.*4616G>T",
"hgvs_p": null,
"transcript": "ENST00000322313.9",
"protein_id": "ENSP00000325377.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1336,
"cds_start": -4,
"cds_end": null,
"cds_length": 4011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9490,
"mane_select": "NM_018383.5",
"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": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR33",
"gene_hgnc_id": 25651,
"hgvs_c": "c.*4616G>T",
"hgvs_p": null,
"transcript": "XM_011511436.2",
"protein_id": "XP_011509738.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1336,
"cds_start": -4,
"cds_end": null,
"cds_length": 4011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9753,
"mane_select": null,
"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": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR33",
"gene_hgnc_id": 25651,
"hgvs_c": "c.*4786G>T",
"hgvs_p": null,
"transcript": "XM_005263697.4",
"protein_id": "XP_005263754.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1133,
"cds_start": -4,
"cds_end": null,
"cds_length": 3402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000293688",
"gene_hgnc_id": null,
"hgvs_c": "n.-247G>T",
"hgvs_p": null,
"transcript": "ENST00000718293.1",
"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": 973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SFT2D3",
"gene_hgnc_id": 28767,
"dbsnp": "rs773717301",
"frequency_reference_population": 0.000006028027,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.0000042522,
"gnomad_genomes_af": 0.0000198318,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3499999940395355,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.26,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.07,
"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_032740.4",
"gene_symbol": "SFT2D3",
"hgnc_id": 28767,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.179C>A",
"hgvs_p": "p.Ser60*"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018383.5",
"gene_symbol": "WDR33",
"hgnc_id": 25651,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*4616G>T",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000718293.1",
"gene_symbol": "ENSG00000293688",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-247G>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
}