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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: X-41578435-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=41578435&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 41578435,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000378163.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "NM_001367721.1",
"protein_id": "NP_001354650.1",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 926,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 1974,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "ENST00000378163.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "ENST00000378163.7",
"protein_id": "ENSP00000367405.1",
"transcript_support_level": 5,
"aa_start": 470,
"aa_end": null,
"aa_length": 926,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 1974,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "NM_001367721.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "ENST00000421587.8",
"protein_id": "ENSP00000400526.4",
"transcript_support_level": 1,
"aa_start": 470,
"aa_end": null,
"aa_length": 903,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 1430,
"cdna_end": null,
"cdna_length": 8220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1390G>A",
"hgvs_p": "p.Gly464Ser",
"transcript": "ENST00000378166.9",
"protein_id": "ENSP00000367408.5",
"transcript_support_level": 1,
"aa_start": 464,
"aa_end": null,
"aa_length": 892,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2679,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1390G>A",
"hgvs_p": "p.Gly464Ser",
"transcript": "ENST00000442742.7",
"protein_id": "ENSP00000398007.3",
"transcript_support_level": 1,
"aa_start": 464,
"aa_end": null,
"aa_length": 880,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2643,
"cdna_start": 1563,
"cdna_end": null,
"cdna_length": 3758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "n.743G>A",
"hgvs_p": null,
"transcript": "ENST00000378179.9",
"protein_id": null,
"transcript_support_level": 1,
"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": 3240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1390G>A",
"hgvs_p": "p.Gly464Ser",
"transcript": "ENST00000645986.2",
"protein_id": "ENSP00000494409.2",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 955,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2868,
"cdna_start": 1919,
"cdna_end": null,
"cdna_length": 4550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1426G>A",
"hgvs_p": "p.Gly476Ser",
"transcript": "ENST00000378168.8",
"protein_id": "ENSP00000367410.4",
"transcript_support_level": 5,
"aa_start": 476,
"aa_end": null,
"aa_length": 927,
"cds_start": 1426,
"cds_end": null,
"cds_length": 2784,
"cdna_start": 1955,
"cdna_end": null,
"cdna_length": 8799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "NM_003688.4",
"protein_id": "NP_003679.2",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 921,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 1974,
"cdna_end": null,
"cdna_length": 8818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "ENST00000645566.1",
"protein_id": "ENSP00000494788.1",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 921,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 4002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1390G>A",
"hgvs_p": "p.Gly464Ser",
"transcript": "NM_001410745.1",
"protein_id": "NP_001397674.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 920,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2763,
"cdna_start": 1956,
"cdna_end": null,
"cdna_length": 8815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1390G>A",
"hgvs_p": "p.Gly464Ser",
"transcript": "ENST00000644219.1",
"protein_id": "ENSP00000495357.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 920,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2763,
"cdna_start": 1563,
"cdna_end": null,
"cdna_length": 6048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "ENST00000378154.3",
"protein_id": "ENSP00000367396.2",
"transcript_support_level": 5,
"aa_start": 470,
"aa_end": null,
"aa_length": 909,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2730,
"cdna_start": 1849,
"cdna_end": null,
"cdna_length": 4037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1390G>A",
"hgvs_p": "p.Gly464Ser",
"transcript": "ENST00000378158.6",
"protein_id": "ENSP00000367400.2",
"transcript_support_level": 5,
"aa_start": 464,
"aa_end": null,
"aa_length": 908,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2727,
"cdna_start": 1546,
"cdna_end": null,
"cdna_length": 3754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1426G>A",
"hgvs_p": "p.Gly476Ser",
"transcript": "ENST00000675354.1",
"protein_id": "ENSP00000502315.1",
"transcript_support_level": null,
"aa_start": 476,
"aa_end": null,
"aa_length": 904,
"cds_start": 1426,
"cds_end": null,
"cds_length": 2715,
"cdna_start": 1955,
"cdna_end": null,
"cdna_length": 8730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "NM_001126054.3",
"protein_id": "NP_001119526.1",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 898,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2697,
"cdna_start": 1974,
"cdna_end": null,
"cdna_length": 8749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "ENST00000646120.2",
"protein_id": "ENSP00000495291.2",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 898,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2697,
"cdna_start": 1427,
"cdna_end": null,
"cdna_length": 3239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1390G>A",
"hgvs_p": "p.Gly464Ser",
"transcript": "NM_001126055.3",
"protein_id": "NP_001119527.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 897,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2694,
"cdna_start": 1956,
"cdna_end": null,
"cdna_length": 8746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1390G>A",
"hgvs_p": "p.Gly464Ser",
"transcript": "ENST00000644347.1",
"protein_id": "ENSP00000494183.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 897,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2694,
"cdna_start": 1571,
"cdna_end": null,
"cdna_length": 8361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.835G>A",
"hgvs_p": "p.Gly279Ser",
"transcript": "ENST00000646087.2",
"protein_id": "ENSP00000495510.2",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 700,
"cds_start": 835,
"cds_end": null,
"cds_length": 2103,
"cdna_start": 969,
"cdna_end": null,
"cdna_length": 3392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.853G>A",
"hgvs_p": "p.Gly285Ser",
"transcript": "ENST00000643043.2",
"protein_id": "ENSP00000493518.2",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 393,
"cds_start": 853,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 906,
"cdna_end": null,
"cdna_length": 1235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "XM_011543993.3",
"protein_id": "XP_011542295.1",
"transcript_support_level": null,
"aa_start": 470,
"aa_end": null,
"aa_length": 926,
"cds_start": 1408,
"cds_end": null,
"cds_length": 2781,
"cdna_start": 1454,
"cdna_end": null,
"cdna_length": 8313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASK",
"gene_hgnc_id": 1497,
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser",
"transcript": "XM_011543994.3",
"protein_id": "XP_011542296.1",
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"aa_start": 470,
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},
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}
],
"gene_symbol": "CASK",
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"dbsnp": "rs1021774904",
"frequency_reference_population": 0.000009183385,
"hom_count_reference_population": 1,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000918339,
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"gnomad_exomes_ac": 10,
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"gnomad_exomes_homalt": 0,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6688710451126099,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.28999999165534973,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.359,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3407,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.487,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.29,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000378163.7",
"gene_symbol": "CASK",
"hgnc_id": 1497,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.1408G>A",
"hgvs_p": "p.Gly470Ser"
}
],
"clinvar_disease": " CASK-related, X-linked,Intellectual disability,Seizure,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Intellectual disability, CASK-related, X-linked|not provided|Seizure",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}