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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: 19-14409052-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=14409052&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 14409052,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005804.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "NM_005804.4",
"protein_id": "NP_005795.2",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 427,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000242776.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005804.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "ENST00000242776.9",
"protein_id": "ENSP00000242776.3",
"transcript_support_level": 1,
"aa_start": 418,
"aa_end": null,
"aa_length": 427,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005804.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000242776.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "n.*173G>A",
"hgvs_p": null,
"transcript": "ENST00000324340.13",
"protein_id": "ENSP00000322749.8",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000324340.13"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "n.1664G>A",
"hgvs_p": null,
"transcript": "ENST00000587730.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000587730.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "n.1754G>A",
"hgvs_p": null,
"transcript": "ENST00000589318.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000589318.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "n.*173G>A",
"hgvs_p": null,
"transcript": "ENST00000324340.13",
"protein_id": "ENSP00000322749.8",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000324340.13"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "ENST00000926037.1",
"protein_id": "ENSP00000596096.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 435,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926037.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "ENST00000898540.1",
"protein_id": "ENSP00000568599.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 427,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898540.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "ENST00000926035.1",
"protein_id": "ENSP00000596094.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 427,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926035.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "ENST00000926036.1",
"protein_id": "ENSP00000596095.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 427,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926036.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "ENST00000926039.1",
"protein_id": "ENSP00000596098.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 427,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926039.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "ENST00000950771.1",
"protein_id": "ENSP00000620830.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 427,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950771.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1219G>A",
"hgvs_p": "p.Asp407Asn",
"transcript": "ENST00000898538.1",
"protein_id": "ENSP00000568597.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 416,
"cds_start": 1219,
"cds_end": null,
"cds_length": 1251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898538.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Asp374Asn",
"transcript": "ENST00000898539.1",
"protein_id": "ENSP00000568598.1",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 383,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898539.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.949G>A",
"hgvs_p": "p.Asp317Asn",
"transcript": "ENST00000926038.1",
"protein_id": "ENSP00000596097.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 326,
"cds_start": 949,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926038.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "XM_011527620.2",
"protein_id": "XP_011525922.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 427,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527620.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "n.*556G>A",
"hgvs_p": null,
"transcript": "ENST00000588692.5",
"protein_id": "ENSP00000467862.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000588692.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "n.1260G>A",
"hgvs_p": null,
"transcript": "NR_046366.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_046366.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"hgvs_c": "n.*556G>A",
"hgvs_p": null,
"transcript": "ENST00000588692.5",
"protein_id": "ENSP00000467862.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000588692.5"
}
],
"gene_symbol": "DDX39A",
"gene_hgnc_id": 17821,
"dbsnp": "rs1360378048",
"frequency_reference_population": 0.0000013680994,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000013681,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6861594915390015,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.128,
"revel_prediction": "Benign",
"alphamissense_score": 0.2147,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.491,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005804.4",
"gene_symbol": "DDX39A",
"hgnc_id": 17821,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn"
}
],
"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
}