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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: 16-89709844-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=89709844&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 89709844,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004913.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1321C>A",
"hgvs_p": "p.Arg441Ser",
"transcript": "NM_004913.3",
"protein_id": "NP_004904.2",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 631,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1358,
"cdna_end": null,
"cdna_length": 2660,
"mane_select": "ENST00000389386.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004913.3"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1321C>A",
"hgvs_p": "p.Arg441Ser",
"transcript": "ENST00000389386.8",
"protein_id": "ENSP00000374037.3",
"transcript_support_level": 1,
"aa_start": 441,
"aa_end": null,
"aa_length": 631,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1358,
"cdna_end": null,
"cdna_length": 2660,
"mane_select": "NM_004913.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389386.8"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1111C>A",
"hgvs_p": "p.Arg371Ser",
"transcript": "ENST00000561976.5",
"protein_id": "ENSP00000454244.1",
"transcript_support_level": 1,
"aa_start": 371,
"aa_end": null,
"aa_length": 561,
"cds_start": 1111,
"cds_end": null,
"cds_length": 1686,
"cdna_start": 1489,
"cdna_end": null,
"cdna_length": 2791,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000561976.5"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1321C>A",
"hgvs_p": "p.Arg441Ser",
"transcript": "ENST00000906741.1",
"protein_id": "ENSP00000576800.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 646,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1941,
"cdna_start": 1653,
"cdna_end": null,
"cdna_length": 3006,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906741.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1366C>A",
"hgvs_p": "p.Arg456Ser",
"transcript": "ENST00000906743.1",
"protein_id": "ENSP00000576802.1",
"transcript_support_level": null,
"aa_start": 456,
"aa_end": null,
"aa_length": 646,
"cds_start": 1366,
"cds_end": null,
"cds_length": 1941,
"cdna_start": 1426,
"cdna_end": null,
"cdna_length": 2728,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906743.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Ser",
"transcript": "ENST00000906740.1",
"protein_id": "ENSP00000576799.1",
"transcript_support_level": null,
"aa_start": 454,
"aa_end": null,
"aa_length": 644,
"cds_start": 1360,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 1823,
"cdna_end": null,
"cdna_length": 3126,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906740.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1315C>A",
"hgvs_p": "p.Arg439Ser",
"transcript": "ENST00000906745.1",
"protein_id": "ENSP00000576804.1",
"transcript_support_level": null,
"aa_start": 439,
"aa_end": null,
"aa_length": 629,
"cds_start": 1315,
"cds_end": null,
"cds_length": 1890,
"cdna_start": 1321,
"cdna_end": null,
"cdna_length": 2622,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906745.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1285C>A",
"hgvs_p": "p.Arg429Ser",
"transcript": "ENST00000962839.1",
"protein_id": "ENSP00000632898.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 619,
"cds_start": 1285,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1290,
"cdna_end": null,
"cdna_length": 2592,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962839.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1282C>A",
"hgvs_p": "p.Arg428Ser",
"transcript": "ENST00000906744.1",
"protein_id": "ENSP00000576803.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 618,
"cds_start": 1282,
"cds_end": null,
"cds_length": 1857,
"cdna_start": 1304,
"cdna_end": null,
"cdna_length": 2606,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906744.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1255C>A",
"hgvs_p": "p.Arg419Ser",
"transcript": "ENST00000962838.1",
"protein_id": "ENSP00000632897.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 609,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1830,
"cdna_start": 1322,
"cdna_end": null,
"cdna_length": 2623,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962838.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1228C>A",
"hgvs_p": "p.Arg410Ser",
"transcript": "ENST00000906742.1",
"protein_id": "ENSP00000576801.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 600,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 1328,
"cdna_end": null,
"cdna_length": 2629,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906742.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1321C>A",
"hgvs_p": "p.Arg441Ser",
"transcript": "ENST00000962837.1",
"protein_id": "ENSP00000632896.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 596,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 1388,
"cdna_end": null,
"cdna_length": 2585,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962837.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.121C>A",
"hgvs_p": "p.Arg41Ser",
"transcript": "ENST00000565023.1",
"protein_id": "ENSP00000455792.1",
"transcript_support_level": 5,
"aa_start": 41,
"aa_end": null,
"aa_length": 231,
"cds_start": 121,
"cds_end": null,
"cds_length": 696,
"cdna_start": 123,
"cdna_end": null,
"cdna_length": 775,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000565023.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1363C>A",
"hgvs_p": "p.Arg455Ser",
"transcript": "XM_047434930.1",
"protein_id": "XP_047290886.1",
"transcript_support_level": null,
"aa_start": 455,
"aa_end": null,
"aa_length": 645,
"cds_start": 1363,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 1400,
"cdna_end": null,
"cdna_length": 2702,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434930.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Ser",
"transcript": "XM_047434931.1",
"protein_id": "XP_047290887.1",
"transcript_support_level": null,
"aa_start": 454,
"aa_end": null,
"aa_length": 644,
"cds_start": 1360,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 1397,
"cdna_end": null,
"cdna_length": 2699,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434931.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1324C>A",
"hgvs_p": "p.Arg442Ser",
"transcript": "XM_005256329.6",
"protein_id": "XP_005256386.1",
"transcript_support_level": null,
"aa_start": 442,
"aa_end": null,
"aa_length": 632,
"cds_start": 1324,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 2663,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005256329.6"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1321C>A",
"hgvs_p": "p.Arg441Ser",
"transcript": "XM_011523476.4",
"protein_id": "XP_011521778.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 631,
"cds_start": 1321,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1358,
"cdna_end": null,
"cdna_length": 2660,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011523476.4"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1318C>A",
"hgvs_p": "p.Arg440Ser",
"transcript": "XM_047434932.1",
"protein_id": "XP_047290888.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 630,
"cds_start": 1318,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1355,
"cdna_end": null,
"cdna_length": 2657,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434932.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1261C>A",
"hgvs_p": "p.Arg421Ser",
"transcript": "XM_047434933.1",
"protein_id": "XP_047290889.1",
"transcript_support_level": null,
"aa_start": 421,
"aa_end": null,
"aa_length": 611,
"cds_start": 1261,
"cds_end": null,
"cds_length": 1836,
"cdna_start": 1265,
"cdna_end": null,
"cdna_length": 2567,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434933.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1258C>A",
"hgvs_p": "p.Arg420Ser",
"transcript": "XM_047434934.1",
"protein_id": "XP_047290890.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 610,
"cds_start": 1258,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 1259,
"cdna_end": null,
"cdna_length": 2561,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434934.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1363C>A",
"hgvs_p": "p.Arg455Ser",
"transcript": "XM_047434935.1",
"protein_id": "XP_047290891.1",
"transcript_support_level": null,
"aa_start": 455,
"aa_end": null,
"aa_length": 610,
"cds_start": 1363,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 1400,
"cdna_end": null,
"cdna_length": 2597,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434935.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS9D1",
"gene_hgnc_id": 13526,
"hgvs_c": "c.1321C>A",
"hgvs_p": "p.Arg441Ser",
"transcript": "XM_047434936.1",
"protein_id": "XP_047290892.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 596,
"cds_start": 1321,
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"feature": "XM_047434936.1"
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{
"aa_ref": "R",
"aa_alt": "S",
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"protein_coding": true,
"strand": false,
"consequences": [
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],
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"exon_count": 15,
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"gene_symbol": "VPS9D1",
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"hgvs_c": "c.1153C>A",
"hgvs_p": "p.Arg385Ser",
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"protein_id": "XP_047290893.1",
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"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434937.1"
}
],
"gene_symbol": "VPS9D1",
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"dbsnp": "rs747712289",
"frequency_reference_population": 6.8423884e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84239e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4637433886528015,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.167,
"revel_prediction": "Benign",
"alphamissense_score": 0.371,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.973,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.05,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004913.3",
"gene_symbol": "VPS9D1",
"hgnc_id": 13526,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1321C>A",
"hgvs_p": "p.Arg441Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}