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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: 2-32064120-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=32064120&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 32064120,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000315285.9",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "NM_014946.4",
"protein_id": "NP_055761.2",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 616,
"cds_start": 289,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 5268,
"mane_select": "ENST00000315285.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000315285.9",
"protein_id": "ENSP00000320885.3",
"transcript_support_level": 1,
"aa_start": 97,
"aa_end": null,
"aa_length": 616,
"cds_start": 289,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 5268,
"mane_select": "NM_014946.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000621856.2",
"protein_id": "ENSP00000482496.2",
"transcript_support_level": 1,
"aa_start": 97,
"aa_end": null,
"aa_length": 615,
"cds_start": 289,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 339,
"cdna_end": null,
"cdna_length": 2084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000713716.1",
"protein_id": "ENSP00000519019.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 651,
"cds_start": 289,
"cds_end": null,
"cds_length": 1956,
"cdna_start": 539,
"cdna_end": null,
"cdna_length": 3484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "NM_001363823.2",
"protein_id": "NP_001350752.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 615,
"cds_start": 289,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 5265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000647133.2",
"protein_id": "ENSP00000493742.2",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 591,
"cds_start": 289,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 289,
"cdna_end": null,
"cdna_length": 2996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "NM_199436.2",
"protein_id": "NP_955468.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 584,
"cds_start": 289,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 5172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000646571.1",
"protein_id": "ENSP00000495015.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 584,
"cds_start": 289,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 5117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "NM_001363875.2",
"protein_id": "NP_001350804.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 583,
"cds_start": 289,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 5169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000642455.1",
"protein_id": "ENSP00000493827.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 583,
"cds_start": 289,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 293,
"cdna_end": null,
"cdna_length": 2107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000644408.2",
"protein_id": "ENSP00000493748.2",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 571,
"cds_start": 289,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 289,
"cdna_end": null,
"cdna_length": 2335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000642281.2",
"protein_id": "ENSP00000496211.2",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 567,
"cds_start": 289,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 289,
"cdna_end": null,
"cdna_length": 2244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.31C>A",
"hgvs_p": "p.Pro11Thr",
"transcript": "ENST00000642999.1",
"protein_id": "ENSP00000496589.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 530,
"cds_start": 31,
"cds_end": null,
"cds_length": 1593,
"cdna_start": 153,
"cdna_end": null,
"cdna_length": 4701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "NM_001377959.1",
"protein_id": "NP_001364888.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 519,
"cds_start": 289,
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"cdna_start": 565,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000642751.2",
"protein_id": "ENSP00000495478.2",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 519,
"cds_start": 289,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 289,
"cdna_end": null,
"cdna_length": 4825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.31C>A",
"hgvs_p": "p.Pro11Thr",
"transcript": "ENST00000644954.1",
"protein_id": "ENSP00000494312.1",
"transcript_support_level": null,
"aa_start": 11,
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"cds_start": 31,
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"cdna_start": 151,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr",
"transcript": "ENST00000645671.2",
"protein_id": "ENSP00000494601.2",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 494,
"cds_start": 289,
"cds_end": null,
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"cdna_start": 289,
"cdna_end": null,
"cdna_length": 1870,
"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": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.289C>A",
"hgvs_p": null,
"transcript": "ENST00000643327.2",
"protein_id": "ENSP00000494170.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 1458,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.289C>A",
"hgvs_p": null,
"transcript": "ENST00000645400.2",
"protein_id": "ENSP00000496306.2",
"transcript_support_level": null,
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"feature": null
},
{
"aa_ref": null,
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"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": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.289C>A",
"hgvs_p": null,
"transcript": "ENST00000646082.2",
"protein_id": "ENSP00000496334.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.289C>A",
"hgvs_p": null,
"transcript": "ENST00000704289.1",
"protein_id": "ENSP00000515816.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2350,
"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": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.289C>A",
"hgvs_p": null,
"transcript": "ENST00000713714.1",
"protein_id": "ENSP00000519017.1",
"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": 5252,
"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": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.289C>A",
"hgvs_p": null,
"transcript": "ENST00000713715.1",
"protein_id": "ENSP00000519018.1",
"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": 5312,
"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": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.289C>A",
"hgvs_p": null,
"transcript": "ENST00000713718.1",
"protein_id": "ENSP00000519021.1",
"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": 5058,
"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": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.31C>A",
"hgvs_p": null,
"transcript": "ENST00000713719.1",
"protein_id": "ENSP00000519022.1",
"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": 5098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"dbsnp": "rs372005558",
"frequency_reference_population": 0.00026807497,
"hom_count_reference_population": 2,
"allele_count_reference_population": 427,
"gnomad_exomes_af": 0.000266532,
"gnomad_genomes_af": 0.00028269,
"gnomad_exomes_ac": 384,
"gnomad_genomes_ac": 43,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.015602290630340576,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.224,
"revel_prediction": "Benign",
"alphamissense_score": 0.0697,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.636,
"phylop100way_prediction": "Benign",
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000315285.9",
"gene_symbol": "SPAST",
"hgnc_id": 11233,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.289C>A",
"hgvs_p": "p.Pro97Thr"
}
],
"clinvar_disease": "Hereditary spastic paraplegia 4,SPAST-related disorder,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Hereditary spastic paraplegia 4|not provided|SPAST-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}