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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: 20-54208114-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=54208114&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 54208114,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_002623.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFDN4",
"gene_hgnc_id": 8868,
"hgvs_c": "c.14T>C",
"hgvs_p": "p.Met5Thr",
"transcript": "NM_002623.4",
"protein_id": "NP_002614.2",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 134,
"cds_start": 14,
"cds_end": null,
"cds_length": 405,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 1230,
"mane_select": "ENST00000371419.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFDN4",
"gene_hgnc_id": 8868,
"hgvs_c": "c.14T>C",
"hgvs_p": "p.Met5Thr",
"transcript": "ENST00000371419.7",
"protein_id": "ENSP00000360473.2",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 134,
"cds_start": 14,
"cds_end": null,
"cds_length": 405,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 1230,
"mane_select": "NM_002623.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFDN4",
"gene_hgnc_id": 8868,
"hgvs_c": "c.14T>C",
"hgvs_p": "p.Met5Thr",
"transcript": "ENST00000715725.2",
"protein_id": "ENSP00000520507.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 134,
"cds_start": 14,
"cds_end": null,
"cds_length": 405,
"cdna_start": 194,
"cdna_end": null,
"cdna_length": 1388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFDN4",
"gene_hgnc_id": 8868,
"hgvs_c": "c.14T>C",
"hgvs_p": "p.Met5Thr",
"transcript": "XM_047440198.1",
"protein_id": "XP_047296154.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 216,
"cds_start": 14,
"cds_end": null,
"cds_length": 651,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 1476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFDN4",
"gene_hgnc_id": 8868,
"hgvs_c": "c.14T>C",
"hgvs_p": "p.Met5Thr",
"transcript": "XM_047440199.1",
"protein_id": "XP_047296155.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 136,
"cds_start": 14,
"cds_end": null,
"cds_length": 411,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFDN4",
"gene_hgnc_id": 8868,
"hgvs_c": "n.14T>C",
"hgvs_p": null,
"transcript": "ENST00000441080.2",
"protein_id": "ENSP00000432441.1",
"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": 579,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PFDN4",
"gene_hgnc_id": 8868,
"hgvs_c": "n.-198T>C",
"hgvs_p": null,
"transcript": "ENST00000487129.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 762,
"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": "PFDN4",
"gene_hgnc_id": 8868,
"hgvs_c": "n.-186T>C",
"hgvs_p": null,
"transcript": "ENST00000493356.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 659,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124904937",
"gene_hgnc_id": null,
"hgvs_c": "n.-73A>G",
"hgvs_p": null,
"transcript": "XR_007067669.1",
"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": 196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PFDN4",
"gene_hgnc_id": 8868,
"dbsnp": "rs1344316136",
"frequency_reference_population": 0.0000044961316,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000427133,
"gnomad_genomes_af": 0.00000657125,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3310413062572479,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.139,
"revel_prediction": "Benign",
"alphamissense_score": 0.4235,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.947,
"phylop100way_prediction": "Benign",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002623.4",
"gene_symbol": "PFDN4",
"hgnc_id": 8868,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.14T>C",
"hgvs_p": "p.Met5Thr"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007067669.1",
"gene_symbol": "LOC124904937",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-73A>G",
"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
}