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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: 19-17843777-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=17843777&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 17843777,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000458235.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Arg103His",
"transcript": "NM_000215.4",
"protein_id": "NP_000206.2",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 1124,
"cds_start": 308,
"cds_end": null,
"cds_length": 3375,
"cdna_start": 358,
"cdna_end": null,
"cdna_length": 5386,
"mane_select": "ENST00000458235.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Arg103His",
"transcript": "ENST00000458235.7",
"protein_id": "ENSP00000391676.1",
"transcript_support_level": 5,
"aa_start": 103,
"aa_end": null,
"aa_length": 1124,
"cds_start": 308,
"cds_end": null,
"cds_length": 3375,
"cdna_start": 358,
"cdna_end": null,
"cdna_length": 5386,
"mane_select": "NM_000215.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Arg103His",
"transcript": "ENST00000527670.5",
"protein_id": "ENSP00000432511.1",
"transcript_support_level": 1,
"aa_start": 103,
"aa_end": null,
"aa_length": 1124,
"cds_start": 308,
"cds_end": null,
"cds_length": 3375,
"cdna_start": 338,
"cdna_end": null,
"cdna_length": 3996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Arg103His",
"transcript": "ENST00000534444.1",
"protein_id": "ENSP00000436421.1",
"transcript_support_level": 1,
"aa_start": 103,
"aa_end": null,
"aa_length": 1094,
"cds_start": 308,
"cds_end": null,
"cds_length": 3285,
"cdna_start": 393,
"cdna_end": null,
"cdna_length": 3612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Arg103His",
"transcript": "NM_001440439.1",
"protein_id": "NP_001427368.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 1124,
"cds_start": 308,
"cds_end": null,
"cds_length": 3375,
"cdna_start": 389,
"cdna_end": null,
"cdna_length": 5417,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Arg103His",
"transcript": "XM_011527991.3",
"protein_id": "XP_011526293.2",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 607,
"cds_start": 308,
"cds_end": null,
"cds_length": 1824,
"cdna_start": 358,
"cdna_end": null,
"cdna_length": 2748,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "n.308G>A",
"hgvs_p": null,
"transcript": "ENST00000526008.6",
"protein_id": "ENSP00000513006.1",
"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": 4115,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "n.398G>A",
"hgvs_p": null,
"transcript": "ENST00000527031.5",
"protein_id": null,
"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": 2809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "n.358G>A",
"hgvs_p": null,
"transcript": "XR_007066796.1",
"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": 2892,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"hgvs_c": "n.324-286G>A",
"hgvs_p": null,
"transcript": "ENST00000528293.1",
"protein_id": null,
"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": 1173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "JAK3",
"gene_hgnc_id": 6193,
"dbsnp": "rs774202259",
"frequency_reference_population": 0.00000681812,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000684303,
"gnomad_genomes_af": 0.0000065786,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9704556465148926,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.984000027179718,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.678,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8417,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.622,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.88,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999992710384505,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000458235.7",
"gene_symbol": "JAK3",
"hgnc_id": 6193,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Arg103His"
}
],
"clinvar_disease": "Severe combined immunodeficiency disease,T-B+ severe combined immunodeficiency due to JAK3 deficiency,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:1",
"phenotype_combined": "not provided|T-B+ severe combined immunodeficiency due to JAK3 deficiency|Severe combined immunodeficiency disease",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}