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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: 2-216039296-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=216039296&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 216039296,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018441.6",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"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": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "c.891T>A",
"hgvs_p": "p.Phe297Leu",
"transcript": "NM_018441.6",
"protein_id": "NP_060911.2",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 303,
"cds_start": 891,
"cds_end": null,
"cds_length": 912,
"cdna_start": 959,
"cdna_end": null,
"cdna_length": 1867,
"mane_select": "ENST00000265322.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018441.6"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"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": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "c.891T>A",
"hgvs_p": "p.Phe297Leu",
"transcript": "ENST00000265322.8",
"protein_id": "ENSP00000265322.7",
"transcript_support_level": 1,
"aa_start": 297,
"aa_end": null,
"aa_length": 303,
"cds_start": 891,
"cds_end": null,
"cds_length": 912,
"cdna_start": 959,
"cdna_end": null,
"cdna_length": 1867,
"mane_select": "NM_018441.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265322.8"
},
{
"aa_ref": "F",
"aa_alt": "L",
"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": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "c.873T>A",
"hgvs_p": "p.Phe291Leu",
"transcript": "ENST00000912895.1",
"protein_id": "ENSP00000582954.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 297,
"cds_start": 873,
"cds_end": null,
"cds_length": 894,
"cdna_start": 900,
"cdna_end": null,
"cdna_length": 1793,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912895.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "c.591T>A",
"hgvs_p": "p.Phe197Leu",
"transcript": "ENST00000896257.1",
"protein_id": "ENSP00000566316.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 203,
"cds_start": 591,
"cds_end": null,
"cds_length": 612,
"cdna_start": 640,
"cdna_end": null,
"cdna_length": 1524,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896257.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "c.453T>A",
"hgvs_p": "p.Phe151Leu",
"transcript": "XM_047445108.1",
"protein_id": "XP_047301064.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 157,
"cds_start": 453,
"cds_end": null,
"cds_length": 474,
"cdna_start": 548,
"cdna_end": null,
"cdna_length": 1456,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445108.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "n.*335T>A",
"hgvs_p": null,
"transcript": "ENST00000442122.5",
"protein_id": "ENSP00000395512.1",
"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": 1100,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000442122.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "n.772T>A",
"hgvs_p": null,
"transcript": "ENST00000461330.5",
"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": 812,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000461330.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "n.959T>A",
"hgvs_p": null,
"transcript": "XR_001738847.3",
"protein_id": null,
"transcript_support_level": null,
"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": 4829,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001738847.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "n.959T>A",
"hgvs_p": null,
"transcript": "XR_007078552.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2495,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007078552.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "n.959T>A",
"hgvs_p": null,
"transcript": "XR_007078553.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2110,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007078553.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"hgvs_c": "n.*335T>A",
"hgvs_p": null,
"transcript": "ENST00000442122.5",
"protein_id": "ENSP00000395512.1",
"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": 1100,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000442122.5"
}
],
"gene_symbol": "PECR",
"gene_hgnc_id": 18281,
"dbsnp": "rs9288513",
"frequency_reference_population": 0.117400184,
"hom_count_reference_population": 13508,
"allele_count_reference_population": 187868,
"gnomad_exomes_af": 0.115098,
"gnomad_genomes_af": 0.139318,
"gnomad_exomes_ac": 166673,
"gnomad_genomes_ac": 21195,
"gnomad_exomes_homalt": 11672,
"gnomad_genomes_homalt": 1836,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004409760236740112,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.166,
"revel_prediction": "Benign",
"alphamissense_score": 0.6442,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.555,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_018441.6",
"gene_symbol": "PECR",
"hgnc_id": 18281,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.891T>A",
"hgvs_p": "p.Phe297Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}