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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: 4-119239836-T-TAG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=119239836&ref=T&alt=TAG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 119239836,
"ref": "T",
"alt": "TAG",
"effect": "frameshift_variant",
"transcript": "NM_019050.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001371395.1",
"protein_id": "NP_001358324.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000692078.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371395.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000692078.1",
"protein_id": "ENSP00000509606.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001371395.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000692078.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000274030.11",
"protein_id": "ENSP00000274030.6",
"transcript_support_level": 1,
"aa_start": 27,
"aa_end": null,
"aa_length": 800,
"cds_start": 80,
"cds_end": null,
"cds_length": 2403,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000274030.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "n.78_79dupAG",
"hgvs_p": null,
"transcript": "ENST00000509769.5",
"protein_id": "ENSP00000426628.1",
"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": "ENST00000509769.5"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001371399.1",
"protein_id": "NP_001358328.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371399.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001389658.1",
"protein_id": "NP_001376587.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001389658.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001389659.1",
"protein_id": "NP_001376588.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001389659.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_019050.3",
"protein_id": "NP_061923.2",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019050.3"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000450251.6",
"protein_id": "ENSP00000409906.1",
"transcript_support_level": 5,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450251.6"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000883044.1",
"protein_id": "ENSP00000553103.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883044.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000971122.1",
"protein_id": "ENSP00000641181.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1073,
"cds_start": 80,
"cds_end": null,
"cds_length": 3222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971122.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000883046.1",
"protein_id": "ENSP00000553105.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1024,
"cds_start": 80,
"cds_end": null,
"cds_length": 3075,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883046.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001389660.1",
"protein_id": "NP_001376589.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1023,
"cds_start": 80,
"cds_end": null,
"cds_length": 3072,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001389660.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000883047.1",
"protein_id": "ENSP00000553106.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1023,
"cds_start": 80,
"cds_end": null,
"cds_length": 3072,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883047.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001371396.1",
"protein_id": "NP_001358325.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1022,
"cds_start": 80,
"cds_end": null,
"cds_length": 3069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371396.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001389661.1",
"protein_id": "NP_001376590.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1022,
"cds_start": 80,
"cds_end": null,
"cds_length": 3069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001389661.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000883045.1",
"protein_id": "ENSP00000553104.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1022,
"cds_start": 80,
"cds_end": null,
"cds_length": 3069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883045.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000916005.1",
"protein_id": "ENSP00000586064.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1022,
"cds_start": 80,
"cds_end": null,
"cds_length": 3069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916005.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000971123.1",
"protein_id": "ENSP00000641182.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1022,
"cds_start": 80,
"cds_end": null,
"cds_length": 3069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971123.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001371397.1",
"protein_id": "NP_001358326.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 800,
"cds_start": 80,
"cds_end": null,
"cds_length": 2403,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371397.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "NM_001371398.1",
"protein_id": "NP_001358327.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 800,
"cds_start": 80,
"cds_end": null,
"cds_length": 2403,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371398.1"
},
{
"aa_ref": "A",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP53",
"gene_hgnc_id": 29255,
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs",
"transcript": "ENST00000688980.1",
"protein_id": "ENSP00000509357.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 767,
"cds_start": 80,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000688980.1"
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"gene_hgnc_id": 29255,
"dbsnp": null,
"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": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -0.181,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_019050.3",
"gene_symbol": "USP53",
"hgnc_id": 29255,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.78_79dupAG",
"hgvs_p": "p.Ala27fs"
}
],
"clinvar_disease": " 7, progressive familial intrahepatic, with or without hearing loss,Cholestasis",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Cholestasis, progressive familial intrahepatic, 7, with or without hearing loss",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}