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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: 10-15103825-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=15103825&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 15103825,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000378197.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "NM_183005.5",
"protein_id": "NP_892117.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 1052,
"cdna_end": null,
"cdna_length": 1484,
"mane_select": "ENST00000378197.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "ENST00000378197.5",
"protein_id": "ENSP00000367439.4",
"transcript_support_level": 1,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 1052,
"cdna_end": null,
"cdna_length": 1484,
"mane_select": "NM_183005.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "ENST00000378202.5",
"protein_id": "ENSP00000367444.5",
"transcript_support_level": 1,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 600,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NMT2",
"gene_hgnc_id": 7858,
"hgvs_c": "n.128-142C>A",
"hgvs_p": null,
"transcript": "ENST00000466201.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 1227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "NM_001097590.3",
"protein_id": "NP_001091059.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 695,
"cdna_end": null,
"cdna_length": 1127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "NM_001265601.2",
"protein_id": "NP_001252530.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 933,
"cdna_end": null,
"cdna_length": 1365,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "NM_006414.5",
"protein_id": "NP_006405.2",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 576,
"cdna_end": null,
"cdna_length": 1008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "ENST00000378203.5",
"protein_id": "ENSP00000367445.1",
"transcript_support_level": 2,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 870,
"cdna_end": null,
"cdna_length": 1296,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "ENST00000616640.1",
"protein_id": "ENSP00000478982.1",
"transcript_support_level": 2,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 1537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "XM_006717363.3",
"protein_id": "XP_006717426.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 1085,
"cdna_end": null,
"cdna_length": 1517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "XM_006717364.5",
"protein_id": "XP_006717427.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "XM_011519293.3",
"protein_id": "XP_011517595.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 966,
"cdna_end": null,
"cdna_length": 1398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "XM_017015479.3",
"protein_id": "XP_016870968.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 1419,
"cdna_end": null,
"cdna_length": 1851,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "XM_017015480.3",
"protein_id": "XP_016870969.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 684,
"cdna_end": null,
"cdna_length": 1116,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe",
"transcript": "XM_017015481.3",
"protein_id": "XP_016870970.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 283,
"cds_start": 511,
"cds_end": null,
"cds_length": 852,
"cdna_start": 1300,
"cdna_end": null,
"cdna_length": 1732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.399+112G>T",
"hgvs_p": null,
"transcript": "ENST00000378201.6",
"protein_id": "ENSP00000367443.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 145,
"cds_start": -4,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "n.162+6427G>T",
"hgvs_p": null,
"transcript": "ENST00000451677.1",
"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": 323,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"hgvs_c": "c.*5G>T",
"hgvs_p": null,
"transcript": "ENST00000441850.1",
"protein_id": "ENSP00000402635.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 167,
"cds_start": -4,
"cds_end": null,
"cds_length": 506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 863,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RPP38",
"gene_hgnc_id": 30329,
"dbsnp": "rs145237477",
"frequency_reference_population": 0.0000055764363,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000547258,
"gnomad_genomes_af": 0.00000657462,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4334980547428131,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.427,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2252,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.528,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000378197.5",
"gene_symbol": "RPP38",
"hgnc_id": 30329,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.511G>T",
"hgvs_p": "p.Val171Phe"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000466201.1",
"gene_symbol": "NMT2",
"hgnc_id": 7858,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.128-142C>A",
"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
}