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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: 4-139351602-CAAAG-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=139351602&ref=CAAAG&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 139351602,
"ref": "CAAAG",
"alt": "C",
"effect": "frameshift_variant,splice_region_variant",
"transcript": "ENST00000296543.10",
"consequences": [
{
"aa_ref": "EK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "c.1009_1012delGAAA",
"hgvs_p": "p.Glu337fs",
"transcript": "NM_057175.5",
"protein_id": "NP_476516.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 866,
"cds_start": 1009,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 6174,
"mane_select": "ENST00000296543.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EK",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "c.1009_1012delGAAA",
"hgvs_p": "p.Glu337fs",
"transcript": "ENST00000296543.10",
"protein_id": "ENSP00000296543.4",
"transcript_support_level": 1,
"aa_start": 337,
"aa_end": null,
"aa_length": 866,
"cds_start": 1009,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 6174,
"mane_select": "NM_057175.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "c.1009_1012delGAAA",
"hgvs_p": "p.Glu337fs",
"transcript": "NM_001410842.1",
"protein_id": "NP_001397771.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 865,
"cds_start": 1009,
"cds_end": null,
"cds_length": 2598,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 6171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "c.1009_1012delGAAA",
"hgvs_p": "p.Glu337fs",
"transcript": "ENST00000398947.1",
"protein_id": "ENSP00000381920.1",
"transcript_support_level": 5,
"aa_start": 337,
"aa_end": null,
"aa_length": 865,
"cds_start": 1009,
"cds_end": null,
"cds_length": 2598,
"cdna_start": 1199,
"cdna_end": null,
"cdna_length": 6072,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "c.877_880delGAAA",
"hgvs_p": "p.Glu293fs",
"transcript": "ENST00000700277.1",
"protein_id": "ENSP00000514913.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 822,
"cds_start": 877,
"cds_end": null,
"cds_length": 2469,
"cdna_start": 1098,
"cdna_end": null,
"cdna_length": 3765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "c.1009_1012delGAAA",
"hgvs_p": "p.Glu337fs",
"transcript": "ENST00000700275.1",
"protein_id": "ENSP00000514910.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 817,
"cds_start": 1009,
"cds_end": null,
"cds_length": 2454,
"cdna_start": 1341,
"cdna_end": null,
"cdna_length": 4023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "n.1009_1012delGAAA",
"hgvs_p": null,
"transcript": "ENST00000468029.2",
"protein_id": "ENSP00000514912.1",
"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": 2019,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "n.845_848delGAAA",
"hgvs_p": null,
"transcript": "ENST00000480277.2",
"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": 852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "n.*515_*518delGAAA",
"hgvs_p": null,
"transcript": "ENST00000700276.1",
"protein_id": "ENSP00000514911.1",
"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": 1783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "n.1186_1189delGAAA",
"hgvs_p": null,
"transcript": "ENST00000700278.1",
"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": 2346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "n.1267_1270delGAAA",
"hgvs_p": null,
"transcript": "ENST00000700279.1",
"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": 2053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"hgvs_c": "n.*515_*518delGAAA",
"hgvs_p": null,
"transcript": "ENST00000700276.1",
"protein_id": "ENSP00000514911.1",
"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": 1783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NAA15",
"gene_hgnc_id": 30782,
"dbsnp": "rs1553996086",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.483,
"phylop100way_prediction": "Pathogenic",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000296543.10",
"gene_symbol": "NAA15",
"hgnc_id": 30782,
"effects": [
"frameshift_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1009_1012delGAAA",
"hgvs_p": "p.Glu337fs"
}
],
"clinvar_disease": " autosomal dominant 50,Inborn genetic diseases,Intellectual disability",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Intellectual disability, autosomal dominant 50|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}