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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: 3-181712380-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=181712380&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 181712380,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003106.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOX2",
"gene_hgnc_id": 11195,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "NM_003106.4",
"protein_id": "NP_003097.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 317,
"cds_start": 20,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000325404.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003106.4"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOX2",
"gene_hgnc_id": 11195,
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met",
"transcript": "ENST00000325404.3",
"protein_id": "ENSP00000323588.1",
"transcript_support_level": 6,
"aa_start": 7,
"aa_end": null,
"aa_length": 317,
"cds_start": 20,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003106.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000325404.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.349+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000466034.7",
"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": "pseudogene",
"feature": "ENST00000466034.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.482-27189C>T",
"hgvs_p": null,
"transcript": "ENST00000476964.6",
"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": "pseudogene",
"feature": "ENST00000476964.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.593+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000491282.6",
"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": "pseudogene",
"feature": "ENST00000491282.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.541-2805C>T",
"hgvs_p": null,
"transcript": "ENST00000498731.6",
"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": "pseudogene",
"feature": "ENST00000498731.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.708+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000460739.6",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000460739.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.473-27189C>T",
"hgvs_p": null,
"transcript": "ENST00000469278.5",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000469278.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.391+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000477928.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000477928.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.309-27189C>T",
"hgvs_p": null,
"transcript": "ENST00000485035.4",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000485035.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.355-2805C>T",
"hgvs_p": null,
"transcript": "ENST00000492337.6",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000492337.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.782+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000493521.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000493521.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.289-78293C>T",
"hgvs_p": null,
"transcript": "ENST00000498226.6",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000498226.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.355+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000593330.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000593330.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.287-2805C>T",
"hgvs_p": null,
"transcript": "ENST00000593549.6",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000593549.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.286+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000595084.3",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000595084.3"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.286+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000595287.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000595287.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.661+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000596250.7",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000596250.7"
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.286+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000597651.6",
"protein_id": null,
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"aa_start": null,
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"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
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"biotype": "pseudogene",
"feature": "ENST00000597651.6"
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.638-2805C>T",
"hgvs_p": null,
"transcript": "ENST00000597828.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
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"aa_length": null,
"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000597828.5"
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.286+12497C>T",
"hgvs_p": null,
"transcript": "ENST00000598474.4",
"protein_id": null,
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"aa_start": null,
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"aa_length": null,
"cds_start": null,
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"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000598474.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.47+12736C>T",
"hgvs_p": null,
"transcript": "ENST00000599082.2",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000599082.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX2-OT",
"gene_hgnc_id": 20209,
"hgvs_c": "n.287-2805C>T",
"hgvs_p": null,
"transcript": "ENST00000600386.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
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"computational_score_selected": 0.5605102777481079,
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"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4572,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.204,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
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"acmg_score": -2,
"acmg_classification": "Likely_benign",
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"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
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"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_003106.4",
"gene_symbol": "SOX2",
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"effects": [
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"inheritance_mode": "AD",
"hgvs_c": "c.20C>T",
"hgvs_p": "p.Thr7Met"
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{
"score": 2,
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"pathogenic_score": 2,
"criteria": [
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"verdict": "Uncertain_significance",
"transcript": "ENST00000466034.7",
"gene_symbol": "SOX2-OT",
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"effects": [
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],
"inheritance_mode": "",
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}
],
"clinvar_disease": "Congenital aniridia,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|Congenital aniridia",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}