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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: 3-9475532-A-AG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=9475532&ref=A&alt=AG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 9475532,
"ref": "A",
"alt": "AG",
"effect": "frameshift_variant",
"transcript": "NM_001437635.1",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3771dupG",
"hgvs_p": "p.Ser1258fs",
"transcript": "NM_001080517.3",
"protein_id": "NP_001073986.1",
"transcript_support_level": null,
"aa_start": 1258,
"aa_end": null,
"aa_length": 1442,
"cds_start": 3772,
"cds_end": null,
"cds_length": 4329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000402198.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001080517.3"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3771dupG",
"hgvs_p": "p.Ser1258fs",
"transcript": "ENST00000402198.7",
"protein_id": "ENSP00000385852.2",
"transcript_support_level": 5,
"aa_start": 1258,
"aa_end": null,
"aa_length": 1442,
"cds_start": 3772,
"cds_end": null,
"cds_length": 4329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001080517.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000402198.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "n.3935dupG",
"hgvs_p": null,
"transcript": "ENST00000493918.5",
"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": "ENST00000493918.5"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3885dupG",
"hgvs_p": "p.Ser1296fs",
"transcript": "NM_001437635.1",
"protein_id": "NP_001424564.1",
"transcript_support_level": null,
"aa_start": 1296,
"aa_end": null,
"aa_length": 1480,
"cds_start": 3886,
"cds_end": null,
"cds_length": 4443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437635.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3867dupG",
"hgvs_p": "p.Ser1290fs",
"transcript": "NM_001437633.1",
"protein_id": "NP_001424562.1",
"transcript_support_level": null,
"aa_start": 1290,
"aa_end": null,
"aa_length": 1474,
"cds_start": 3868,
"cds_end": null,
"cds_length": 4425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437633.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3867dupG",
"hgvs_p": "p.Ser1290fs",
"transcript": "ENST00000682536.1",
"protein_id": "ENSP00000507956.1",
"transcript_support_level": null,
"aa_start": 1290,
"aa_end": null,
"aa_length": 1474,
"cds_start": 3868,
"cds_end": null,
"cds_length": 4425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682536.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3843dupG",
"hgvs_p": "p.Ser1282fs",
"transcript": "ENST00000866906.1",
"protein_id": "ENSP00000536965.1",
"transcript_support_level": null,
"aa_start": 1282,
"aa_end": null,
"aa_length": 1466,
"cds_start": 3844,
"cds_end": null,
"cds_length": 4401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866906.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3828dupG",
"hgvs_p": "p.Ser1277fs",
"transcript": "NM_001437643.1",
"protein_id": "NP_001424572.1",
"transcript_support_level": null,
"aa_start": 1277,
"aa_end": null,
"aa_length": 1461,
"cds_start": 3829,
"cds_end": null,
"cds_length": 4386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437643.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3828dupG",
"hgvs_p": "p.Ser1277fs",
"transcript": "ENST00000407969.5",
"protein_id": "ENSP00000384114.1",
"transcript_support_level": 5,
"aa_start": 1277,
"aa_end": null,
"aa_length": 1461,
"cds_start": 3829,
"cds_end": null,
"cds_length": 4386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000407969.5"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3825dupG",
"hgvs_p": "p.Ser1276fs",
"transcript": "ENST00000866907.1",
"protein_id": "ENSP00000536966.1",
"transcript_support_level": null,
"aa_start": 1276,
"aa_end": null,
"aa_length": 1460,
"cds_start": 3826,
"cds_end": null,
"cds_length": 4383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866907.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3810dupG",
"hgvs_p": "p.Ser1271fs",
"transcript": "NM_001437701.1",
"protein_id": "NP_001424630.1",
"transcript_support_level": null,
"aa_start": 1271,
"aa_end": null,
"aa_length": 1455,
"cds_start": 3811,
"cds_end": null,
"cds_length": 4368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437701.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3810dupG",
"hgvs_p": "p.Ser1271fs",
"transcript": "ENST00000866905.1",
"protein_id": "ENSP00000536964.1",
"transcript_support_level": null,
"aa_start": 1271,
"aa_end": null,
"aa_length": 1455,
"cds_start": 3811,
"cds_end": null,
"cds_length": 4368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866905.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3771dupG",
"hgvs_p": "p.Ser1258fs",
"transcript": "ENST00000406341.5",
"protein_id": "ENSP00000383939.1",
"transcript_support_level": 5,
"aa_start": 1258,
"aa_end": null,
"aa_length": 1442,
"cds_start": 3772,
"cds_end": null,
"cds_length": 4329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000406341.5"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3477dupG",
"hgvs_p": "p.Ser1160fs",
"transcript": "NM_001292043.2",
"protein_id": "NP_001278972.1",
"transcript_support_level": null,
"aa_start": 1160,
"aa_end": null,
"aa_length": 1344,
"cds_start": 3478,
"cds_end": null,
"cds_length": 4035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001292043.2"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3477dupG",
"hgvs_p": "p.Ser1160fs",
"transcript": "NM_001349451.2",
"protein_id": "NP_001336380.1",
"transcript_support_level": null,
"aa_start": 1160,
"aa_end": null,
"aa_length": 1344,
"cds_start": 3478,
"cds_end": null,
"cds_length": 4035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349451.2"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3945dupG",
"hgvs_p": "p.Ser1316fs",
"transcript": "XM_047448466.1",
"protein_id": "XP_047304422.1",
"transcript_support_level": null,
"aa_start": 1316,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3946,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448466.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3945dupG",
"hgvs_p": "p.Ser1316fs",
"transcript": "XM_047448467.1",
"protein_id": "XP_047304423.1",
"transcript_support_level": null,
"aa_start": 1316,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3946,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448467.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3945dupG",
"hgvs_p": "p.Ser1316fs",
"transcript": "XM_047448468.1",
"protein_id": "XP_047304424.1",
"transcript_support_level": null,
"aa_start": 1316,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3946,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448468.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3945dupG",
"hgvs_p": "p.Ser1316fs",
"transcript": "XM_047448469.1",
"protein_id": "XP_047304425.1",
"transcript_support_level": null,
"aa_start": 1316,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3946,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448469.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3945dupG",
"hgvs_p": "p.Ser1316fs",
"transcript": "XM_047448470.1",
"protein_id": "XP_047304426.1",
"transcript_support_level": null,
"aa_start": 1316,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3946,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448470.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3945dupG",
"hgvs_p": "p.Ser1316fs",
"transcript": "XM_047448471.1",
"protein_id": "XP_047304427.1",
"transcript_support_level": null,
"aa_start": 1316,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3946,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448471.1"
},
{
"aa_ref": "S",
"aa_alt": "E?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD5",
"gene_hgnc_id": 25566,
"hgvs_c": "c.3945dupG",
"hgvs_p": "p.Ser1316fs",
"transcript": "XM_047448472.1",
"protein_id": "XP_047304428.1",
"transcript_support_level": null,
"aa_start": 1316,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3946,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
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],
"gene_symbol": "SETD5",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
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"gnomad_exomes_homalt": null,
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"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": 2.524,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"apogee2_score": null,
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"mitotip_score": null,
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"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001437635.1",
"gene_symbol": "SETD5",
"hgnc_id": 25566,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3885dupG",
"hgvs_p": "p.Ser1296fs"
}
],
"clinvar_disease": "Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}