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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: 10-101010521-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=101010521&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 101010521,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000619208.6",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2368A>G",
"hgvs_p": "p.Lys790Glu",
"transcript": "NM_001195263.2",
"protein_id": "NP_001182192.1",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2368,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 2590,
"cdna_end": null,
"cdna_length": 4112,
"mane_select": "ENST00000619208.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2368A>G",
"hgvs_p": "p.Lys790Glu",
"transcript": "ENST00000619208.6",
"protein_id": "ENSP00000480489.1",
"transcript_support_level": 5,
"aa_start": 790,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2368,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 2590,
"cdna_end": null,
"cdna_length": 4112,
"mane_select": "NM_001195263.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2365A>G",
"hgvs_p": "p.Lys789Glu",
"transcript": "NM_001437429.1",
"protein_id": "NP_001424358.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2365,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 2587,
"cdna_end": null,
"cdna_length": 4109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2368A>G",
"hgvs_p": "p.Lys790Glu",
"transcript": "XM_011540177.4",
"protein_id": "XP_011538479.1",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2368,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 2763,
"cdna_end": null,
"cdna_length": 4285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.2368A>G",
"hgvs_p": "p.Lys790Glu",
"transcript": "XM_047425767.1",
"protein_id": "XP_047281723.1",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2368,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 3151,
"cdna_end": null,
"cdna_length": 4673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "n.*2315A>G",
"hgvs_p": null,
"transcript": "ENST00000474125.7",
"protein_id": "ENSP00000474447.1",
"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": 4306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "n.*2315A>G",
"hgvs_p": null,
"transcript": "ENST00000474125.7",
"protein_id": "ENSP00000474447.1",
"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": 4306,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"hgvs_c": "c.*330A>G",
"hgvs_p": null,
"transcript": "XM_011540179.4",
"protein_id": "XP_011538481.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 677,
"cds_start": -4,
"cds_end": null,
"cds_length": 2034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDZD7",
"gene_hgnc_id": 26257,
"dbsnp": "rs111287837",
"frequency_reference_population": 0.03847094,
"hom_count_reference_population": 2089,
"allele_count_reference_population": 58874,
"gnomad_exomes_af": 0.0347914,
"gnomad_genomes_af": 0.0722137,
"gnomad_exomes_ac": 48008,
"gnomad_genomes_ac": 10866,
"gnomad_exomes_homalt": 1333,
"gnomad_genomes_homalt": 756,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.001609116792678833,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": 0.106,
"revel_prediction": "Benign",
"alphamissense_score": 0.2345,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.911,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000619208.6",
"gene_symbol": "PDZD7",
"hgnc_id": 26257,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.2368A>G",
"hgvs_p": "p.Lys790Glu"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}