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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: 2-178461089-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=178461089&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 178461089,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000644580.2",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.874G>A",
"hgvs_p": "p.Gly292Arg",
"transcript": "NM_001042702.5",
"protein_id": "NP_001036167.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 352,
"cds_start": 874,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 1288,
"cdna_end": null,
"cdna_length": 2301,
"mane_select": "ENST00000644580.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.874G>A",
"hgvs_p": "p.Gly292Arg",
"transcript": "ENST00000644580.2",
"protein_id": "ENSP00000495855.2",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 352,
"cds_start": 874,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 1288,
"cdna_end": null,
"cdna_length": 2301,
"mane_select": "NM_001042702.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.874G>A",
"hgvs_p": "p.Gly292Arg",
"transcript": "ENST00000375129.8",
"protein_id": "ENSP00000364271.4",
"transcript_support_level": 1,
"aa_start": 292,
"aa_end": null,
"aa_length": 352,
"cds_start": 874,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 1017,
"cdna_end": null,
"cdna_length": 1202,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "n.1744G>A",
"hgvs_p": null,
"transcript": "ENST00000437056.5",
"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": 1942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.883G>A",
"hgvs_p": "p.Gly295Arg",
"transcript": "NM_001353775.2",
"protein_id": "NP_001340704.1",
"transcript_support_level": null,
"aa_start": 295,
"aa_end": null,
"aa_length": 355,
"cds_start": 883,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 1121,
"cdna_end": null,
"cdna_length": 2134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.880G>A",
"hgvs_p": "p.Gly294Arg",
"transcript": "NM_001353776.2",
"protein_id": "NP_001340705.1",
"transcript_support_level": null,
"aa_start": 294,
"aa_end": null,
"aa_length": 354,
"cds_start": 880,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 980,
"cdna_end": null,
"cdna_length": 1993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.874G>A",
"hgvs_p": "p.Gly292Arg",
"transcript": "NM_001369912.1",
"protein_id": "NP_001356841.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 352,
"cds_start": 874,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 1045,
"cdna_end": null,
"cdna_length": 1522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.775G>A",
"hgvs_p": "p.Gly259Arg",
"transcript": "ENST00000645572.1",
"protein_id": "ENSP00000494301.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 299,
"cds_start": 775,
"cds_end": null,
"cds_length": 901,
"cdna_start": 1780,
"cdna_end": null,
"cdna_length": 1906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Gly133Arg",
"transcript": "NM_001353777.1",
"protein_id": "NP_001340706.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 193,
"cds_start": 397,
"cds_end": null,
"cds_length": 582,
"cdna_start": 1065,
"cdna_end": null,
"cdna_length": 1542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Gly133Arg",
"transcript": "NM_001353778.2",
"protein_id": "NP_001340707.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 193,
"cds_start": 397,
"cds_end": null,
"cds_length": 582,
"cdna_start": 1247,
"cdna_end": null,
"cdna_length": 2260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Gly133Arg",
"transcript": "ENST00000642192.1",
"protein_id": "ENSP00000494225.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 193,
"cds_start": 397,
"cds_end": null,
"cds_length": 582,
"cdna_start": 866,
"cdna_end": null,
"cdna_length": 1186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Gly133Arg",
"transcript": "ENST00000642492.1",
"protein_id": "ENSP00000496267.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 193,
"cds_start": 397,
"cds_end": null,
"cds_length": 582,
"cdna_start": 1378,
"cdna_end": null,
"cdna_length": 1581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Gly133Arg",
"transcript": "ENST00000645817.1",
"protein_id": "ENSP00000495731.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 193,
"cds_start": 397,
"cds_end": null,
"cds_length": 582,
"cdna_start": 1070,
"cdna_end": null,
"cdna_length": 1268,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Gly133Arg",
"transcript": "ENST00000647226.1",
"protein_id": "ENSP00000496024.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 193,
"cds_start": 397,
"cds_end": null,
"cds_length": 582,
"cdna_start": 984,
"cdna_end": null,
"cdna_length": 1289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.979G>A",
"hgvs_p": "p.Gly327Arg",
"transcript": "XM_017004221.3",
"protein_id": "XP_016859710.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 387,
"cds_start": 979,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1079,
"cdna_end": null,
"cdna_length": 2092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.*129G>A",
"hgvs_p": null,
"transcript": "ENST00000442710.5",
"protein_id": "ENSP00000410776.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": -4,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"hgvs_c": "c.*104G>A",
"hgvs_p": null,
"transcript": "ENST00000642762.1",
"protein_id": "ENSP00000496028.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 56,
"cds_start": -4,
"cds_end": null,
"cds_length": 171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PJVK",
"gene_hgnc_id": 29502,
"dbsnp": "rs79399438",
"frequency_reference_population": 0.026062023,
"hom_count_reference_population": 897,
"allele_count_reference_population": 42064,
"gnomad_exomes_af": 0.0259498,
"gnomad_genomes_af": 0.0271403,
"gnomad_exomes_ac": 37934,
"gnomad_genomes_ac": 4130,
"gnomad_exomes_homalt": 811,
"gnomad_genomes_homalt": 86,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0017353296279907227,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.169,
"revel_prediction": "Benign",
"alphamissense_score": 0.3008,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.519,
"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": -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": "ENST00000644580.2",
"gene_symbol": "PJVK",
"hgnc_id": 29502,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.874G>A",
"hgvs_p": "p.Gly292Arg"
}
],
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 59,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:7",
"phenotype_combined": "not specified|Autosomal recessive nonsyndromic hearing loss 59|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}