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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: 16-15363750-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=15363750&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 15363750,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000360151.9",
"consequences": [
{
"aa_ref": "P",
"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": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.962C>T",
"hgvs_p": "p.Pro321Leu",
"transcript": "NM_001277325.2",
"protein_id": "NP_001264254.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 350,
"cds_start": 962,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 1084,
"mane_select": "ENST00000360151.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.962C>T",
"hgvs_p": "p.Pro321Leu",
"transcript": "ENST00000360151.9",
"protein_id": "ENSP00000433597.1",
"transcript_support_level": 1,
"aa_start": 321,
"aa_end": null,
"aa_length": 350,
"cds_start": 962,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 1084,
"mane_select": "NM_001277325.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.1106C>T",
"hgvs_p": "p.Pro369Leu",
"transcript": "XM_047433463.1",
"protein_id": "XP_047289419.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 398,
"cds_start": 1106,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 1222,
"cdna_end": null,
"cdna_length": 1348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.1043C>T",
"hgvs_p": "p.Pro348Leu",
"transcript": "XM_047433460.1",
"protein_id": "XP_047289416.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 377,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 1539,
"cdna_end": null,
"cdna_length": 1665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Pro340Leu",
"transcript": "XM_024450132.2",
"protein_id": "XP_024305900.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 369,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1110,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 1398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Pro340Leu",
"transcript": "XM_047433461.1",
"protein_id": "XP_047289417.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 369,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1110,
"cdna_start": 1278,
"cdna_end": null,
"cdna_length": 1404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Pro340Leu",
"transcript": "XM_047433462.1",
"protein_id": "XP_047289418.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 369,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1110,
"cdna_start": 1189,
"cdna_end": null,
"cdna_length": 1315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.974C>T",
"hgvs_p": "p.Pro325Leu",
"transcript": "XM_047433464.1",
"protein_id": "XP_047289420.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 354,
"cds_start": 974,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 989,
"cdna_end": null,
"cdna_length": 1115,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "n.2336C>T",
"hgvs_p": null,
"transcript": "XR_932754.4",
"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": 2462,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.*333C>T",
"hgvs_p": null,
"transcript": "NM_001351200.1",
"protein_id": "NP_001338129.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 232,
"cds_start": -4,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1158,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.*333C>T",
"hgvs_p": null,
"transcript": "XM_011522336.4",
"protein_id": "XP_011520638.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 280,
"cds_start": -4,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.*1126C>T",
"hgvs_p": null,
"transcript": "XM_047433465.1",
"protein_id": "XP_047289421.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 280,
"cds_start": -4,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"hgvs_c": "c.*1126C>T",
"hgvs_p": null,
"transcript": "XM_047433467.1",
"protein_id": "XP_047289423.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 232,
"cds_start": -4,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPIPA5",
"gene_hgnc_id": 41980,
"dbsnp": "rs886037884",
"frequency_reference_population": 0.00005152762,
"hom_count_reference_population": 3,
"allele_count_reference_population": 73,
"gnomad_exomes_af": 0.0000472591,
"gnomad_genomes_af": 0.0000952699,
"gnomad_exomes_ac": 61,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.138008713722229,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.089,
"revel_prediction": "Benign",
"alphamissense_score": 0.1048,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000360151.9",
"gene_symbol": "NPIPA5",
"hgnc_id": 41980,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.962C>T",
"hgvs_p": "p.Pro321Leu"
}
],
"clinvar_disease": "Oromandibular-limb hypogenesis spectrum,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Oromandibular-limb hypogenesis spectrum|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}