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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: 2-32116163-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=32116163&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 32116163,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000315285.9",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.1049C>T",
"hgvs_p": "p.Ala350Val",
"transcript": "NM_014946.4",
"protein_id": "NP_055761.2",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 616,
"cds_start": 1049,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1325,
"cdna_end": null,
"cdna_length": 5268,
"mane_select": "ENST00000315285.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.1049C>T",
"hgvs_p": "p.Ala350Val",
"transcript": "ENST00000315285.9",
"protein_id": "ENSP00000320885.3",
"transcript_support_level": 1,
"aa_start": 350,
"aa_end": null,
"aa_length": 616,
"cds_start": 1049,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1325,
"cdna_end": null,
"cdna_length": 5268,
"mane_select": "NM_014946.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.1046C>T",
"hgvs_p": "p.Ala349Val",
"transcript": "ENST00000621856.2",
"protein_id": "ENSP00000482496.2",
"transcript_support_level": 1,
"aa_start": 349,
"aa_end": null,
"aa_length": 615,
"cds_start": 1046,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 1096,
"cdna_end": null,
"cdna_length": 2084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.1154C>T",
"hgvs_p": "p.Ala385Val",
"transcript": "ENST00000713716.1",
"protein_id": "ENSP00000519019.1",
"transcript_support_level": null,
"aa_start": 385,
"aa_end": null,
"aa_length": 651,
"cds_start": 1154,
"cds_end": null,
"cds_length": 1956,
"cdna_start": 1404,
"cdna_end": null,
"cdna_length": 3484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.1046C>T",
"hgvs_p": "p.Ala349Val",
"transcript": "NM_001363823.2",
"protein_id": "NP_001350752.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 615,
"cds_start": 1046,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 1322,
"cdna_end": null,
"cdna_length": 5265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.1049C>T",
"hgvs_p": "p.Ala350Val",
"transcript": "ENST00000647133.2",
"protein_id": "ENSP00000493742.2",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 591,
"cds_start": 1049,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 1049,
"cdna_end": null,
"cdna_length": 2996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.953C>T",
"hgvs_p": "p.Ala318Val",
"transcript": "NM_199436.2",
"protein_id": "NP_955468.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 584,
"cds_start": 953,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 5172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.953C>T",
"hgvs_p": "p.Ala318Val",
"transcript": "ENST00000646571.1",
"protein_id": "ENSP00000495015.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 584,
"cds_start": 953,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 1174,
"cdna_end": null,
"cdna_length": 5117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.950C>T",
"hgvs_p": "p.Ala317Val",
"transcript": "NM_001363875.2",
"protein_id": "NP_001350804.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 583,
"cds_start": 950,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 1226,
"cdna_end": null,
"cdna_length": 5169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.950C>T",
"hgvs_p": "p.Ala317Val",
"transcript": "ENST00000642455.1",
"protein_id": "ENSP00000493827.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 583,
"cds_start": 950,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 954,
"cdna_end": null,
"cdna_length": 2107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.1049C>T",
"hgvs_p": "p.Ala350Val",
"transcript": "ENST00000644408.2",
"protein_id": "ENSP00000493748.2",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 571,
"cds_start": 1049,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 1049,
"cdna_end": null,
"cdna_length": 2335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.1049C>T",
"hgvs_p": "p.Ala350Val",
"transcript": "ENST00000642281.2",
"protein_id": "ENSP00000496211.2",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 567,
"cds_start": 1049,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 1049,
"cdna_end": null,
"cdna_length": 2244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.791C>T",
"hgvs_p": "p.Ala264Val",
"transcript": "ENST00000642999.1",
"protein_id": "ENSP00000496589.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 530,
"cds_start": 791,
"cds_end": null,
"cds_length": 1593,
"cdna_start": 913,
"cdna_end": null,
"cdna_length": 4701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.953C>T",
"hgvs_p": "p.Ala318Val",
"transcript": "NM_001377959.1",
"protein_id": "NP_001364888.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 519,
"cds_start": 953,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 5101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.953C>T",
"hgvs_p": "p.Ala318Val",
"transcript": "ENST00000642751.2",
"protein_id": "ENSP00000495478.2",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 519,
"cds_start": 953,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 953,
"cdna_end": null,
"cdna_length": 4825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.695C>T",
"hgvs_p": "p.Ala232Val",
"transcript": "ENST00000644954.1",
"protein_id": "ENSP00000494312.1",
"transcript_support_level": null,
"aa_start": 232,
"aa_end": null,
"aa_length": 498,
"cds_start": 695,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 815,
"cdna_end": null,
"cdna_length": 4732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.878C>T",
"hgvs_p": "p.Ala293Val",
"transcript": "ENST00000645671.2",
"protein_id": "ENSP00000494601.2",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 494,
"cds_start": 878,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 878,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Ala132Val",
"transcript": "ENST00000645730.1",
"protein_id": "ENSP00000496072.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 341,
"cds_start": 395,
"cds_end": null,
"cds_length": 1028,
"cdna_start": 396,
"cdna_end": null,
"cdna_length": 1029,
"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": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.1049C>T",
"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,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"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": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.*159C>T",
"hgvs_p": null,
"transcript": "ENST00000646082.2",
"protein_id": "ENSP00000496334.2",
"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": 1802,
"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": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.741C>T",
"hgvs_p": null,
"transcript": "ENST00000647007.1",
"protein_id": null,
"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": 1767,
"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": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.*709C>T",
"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,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"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": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAST",
"gene_hgnc_id": 11233,
"hgvs_c": "n.*411C>T",
"hgvs_p": null,
"transcript": "ENST00000713714.1",
"protein_id": "ENSP00000519017.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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],
"gene_symbol": "SPAST",
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"dbsnp": "rs1060502231",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
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"gnomad_genomes_ac": null,
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"gnomad_mito_homoplasmic": null,
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"computational_score_selected": 0.7989352941513062,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.787,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7779,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.025,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"mitotip_score": null,
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"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
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"PM2",
"PP2",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000315285.9",
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"effects": [
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],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1049C>T",
"hgvs_p": "p.Ala350Val"
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],
"clinvar_disease": "Hereditary spastic paraplegia 4,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:1",
"phenotype_combined": "Hereditary spastic paraplegia 4|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}