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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: 4-158715644-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=158715644&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 158715644,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005038.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.563A>G",
"hgvs_p": "p.Asp188Gly",
"transcript": "NM_005038.3",
"protein_id": "NP_005029.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 370,
"cds_start": 563,
"cds_end": null,
"cds_length": 1113,
"cdna_start": 671,
"cdna_end": null,
"cdna_length": 1830,
"mane_select": "ENST00000307720.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005038.3"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.563A>G",
"hgvs_p": "p.Asp188Gly",
"transcript": "ENST00000307720.4",
"protein_id": "ENSP00000303754.3",
"transcript_support_level": 1,
"aa_start": 188,
"aa_end": null,
"aa_length": 370,
"cds_start": 563,
"cds_end": null,
"cds_length": 1113,
"cdna_start": 671,
"cdna_end": null,
"cdna_length": 1830,
"mane_select": "NM_005038.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307720.4"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.545A>G",
"hgvs_p": "p.Asp182Gly",
"transcript": "ENST00000877683.1",
"protein_id": "ENSP00000547742.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 364,
"cds_start": 545,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 630,
"cdna_end": null,
"cdna_length": 1782,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877683.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.530A>G",
"hgvs_p": "p.Asp177Gly",
"transcript": "ENST00000877682.1",
"protein_id": "ENSP00000547741.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 359,
"cds_start": 530,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 641,
"cdna_end": null,
"cdna_length": 1790,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877682.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.503A>G",
"hgvs_p": "p.Asp168Gly",
"transcript": "ENST00000914202.1",
"protein_id": "ENSP00000584261.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 350,
"cds_start": 503,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 601,
"cdna_end": null,
"cdna_length": 1753,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914202.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.374A>G",
"hgvs_p": "p.Asp125Gly",
"transcript": "ENST00000914203.1",
"protein_id": "ENSP00000584262.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 307,
"cds_start": 374,
"cds_end": null,
"cds_length": 924,
"cdna_start": 449,
"cdna_end": null,
"cdna_length": 1606,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914203.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.*10A>G",
"hgvs_p": null,
"transcript": "XM_047415844.1",
"protein_id": "XP_047271800.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 178,
"cds_start": null,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 672,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047415844.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.523-241A>G",
"hgvs_p": null,
"transcript": "ENST00000914201.1",
"protein_id": "ENSP00000584260.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 329,
"cds_start": null,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1710,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914201.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "c.522+1368A>G",
"hgvs_p": null,
"transcript": "ENST00000953196.1",
"protein_id": "ENSP00000623255.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 246,
"cds_start": null,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1427,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953196.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "n.*10A>G",
"hgvs_p": null,
"transcript": "ENST00000512699.1",
"protein_id": "ENSP00000423207.1",
"transcript_support_level": 3,
"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": 594,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000512699.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"hgvs_c": "n.*10A>G",
"hgvs_p": null,
"transcript": "ENST00000512699.1",
"protein_id": "ENSP00000423207.1",
"transcript_support_level": 3,
"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": 594,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000512699.1"
}
],
"gene_symbol": "PPID",
"gene_hgnc_id": 9257,
"dbsnp": "rs1365193739",
"frequency_reference_population": 0.0000065698705,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.00000656987,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.27301380038261414,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.164,
"revel_prediction": "Benign",
"alphamissense_score": 0.0867,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.369,
"phylop100way_prediction": "Uncertain_significance",
"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_005038.3",
"gene_symbol": "PPID",
"hgnc_id": 9257,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.563A>G",
"hgvs_p": "p.Asp188Gly"
}
],
"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
}