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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: 4-169537893-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=169537893&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 169537893,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001199397.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "NM_001199397.3",
"protein_id": "NP_001186326.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1286,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000507142.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199397.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "ENST00000507142.6",
"protein_id": "ENSP00000424757.2",
"transcript_support_level": 1,
"aa_start": 527,
"aa_end": null,
"aa_length": 1286,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001199397.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507142.6"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "ENST00000439128.6",
"protein_id": "ENSP00000408020.2",
"transcript_support_level": 1,
"aa_start": 527,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000439128.6"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1449T>C",
"hgvs_p": "p.Ala483Ala",
"transcript": "ENST00000511633.5",
"protein_id": "ENSP00000423332.1",
"transcript_support_level": 1,
"aa_start": 483,
"aa_end": null,
"aa_length": 1242,
"cds_start": 1449,
"cds_end": null,
"cds_length": 3729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511633.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1449T>C",
"hgvs_p": "p.Ala483Ala",
"transcript": "ENST00000510533.5",
"protein_id": "ENSP00000427653.1",
"transcript_support_level": 1,
"aa_start": 483,
"aa_end": null,
"aa_length": 1214,
"cds_start": 1449,
"cds_end": null,
"cds_length": 3645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000510533.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1374T>C",
"hgvs_p": "p.Ala458Ala",
"transcript": "ENST00000512193.5",
"protein_id": "ENSP00000424938.1",
"transcript_support_level": 1,
"aa_start": 458,
"aa_end": null,
"aa_length": 1189,
"cds_start": 1374,
"cds_end": null,
"cds_length": 3570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512193.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "NM_001374418.1",
"protein_id": "NP_001361347.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1286,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374418.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "ENST00000937788.1",
"protein_id": "ENSP00000607847.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1286,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937788.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1608T>C",
"hgvs_p": "p.Ala536Ala",
"transcript": "ENST00000687643.1",
"protein_id": "ENSP00000509309.1",
"transcript_support_level": null,
"aa_start": 536,
"aa_end": null,
"aa_length": 1267,
"cds_start": 1608,
"cds_end": null,
"cds_length": 3804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000687643.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "NM_001374419.1",
"protein_id": "NP_001361348.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374419.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "NM_012224.4",
"protein_id": "NP_036356.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012224.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "ENST00000859054.1",
"protein_id": "ENSP00000529113.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859054.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1449T>C",
"hgvs_p": "p.Ala483Ala",
"transcript": "NM_001199398.3",
"protein_id": "NP_001186327.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 1242,
"cds_start": 1449,
"cds_end": null,
"cds_length": 3729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199398.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1530T>C",
"hgvs_p": "p.Ala510Ala",
"transcript": "NM_001374420.1",
"protein_id": "NP_001361349.1",
"transcript_support_level": null,
"aa_start": 510,
"aa_end": null,
"aa_length": 1241,
"cds_start": 1530,
"cds_end": null,
"cds_length": 3726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374420.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1497T>C",
"hgvs_p": "p.Ala499Ala",
"transcript": "ENST00000685111.1",
"protein_id": "ENSP00000508844.1",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 1230,
"cds_start": 1497,
"cds_end": null,
"cds_length": 3693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000685111.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "NM_001440620.1",
"protein_id": "NP_001427549.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1227,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440620.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1449T>C",
"hgvs_p": "p.Ala483Ala",
"transcript": "NM_001199400.3",
"protein_id": "NP_001186329.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 1214,
"cds_start": 1449,
"cds_end": null,
"cds_length": 3645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199400.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1449T>C",
"hgvs_p": "p.Ala483Ala",
"transcript": "ENST00000859053.1",
"protein_id": "ENSP00000529112.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 1214,
"cds_start": 1449,
"cds_end": null,
"cds_length": 3645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859053.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala",
"transcript": "NM_001440621.1",
"protein_id": "NP_001427550.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1199,
"cds_start": 1581,
"cds_end": null,
"cds_length": 3600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440621.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1374T>C",
"hgvs_p": "p.Ala458Ala",
"transcript": "NM_001199399.3",
"protein_id": "NP_001186328.1",
"transcript_support_level": null,
"aa_start": 458,
"aa_end": null,
"aa_length": 1189,
"cds_start": 1374,
"cds_end": null,
"cds_length": 3570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199399.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1449T>C",
"hgvs_p": "p.Ala483Ala",
"transcript": "NM_001440622.1",
"protein_id": "NP_001427551.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 1183,
"cds_start": 1449,
"cds_end": null,
"cds_length": 3552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440622.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "c.1449T>C",
"hgvs_p": "p.Ala483Ala",
"transcript": "NM_001440623.1",
"protein_id": "NP_001427552.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 1155,
"cds_start": 1449,
"cds_end": null,
"cds_length": 3468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
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},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"hgvs_c": "n.*599T>C",
"hgvs_p": null,
"transcript": "ENST00000693604.1",
"protein_id": "ENSP00000509917.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000693604.1"
}
],
"gene_symbol": "NEK1",
"gene_hgnc_id": 7744,
"dbsnp": "rs184804243",
"frequency_reference_population": 0.0002936072,
"hom_count_reference_population": 1,
"allele_count_reference_population": 471,
"gnomad_exomes_af": 0.00014395,
"gnomad_genomes_af": 0.00172045,
"gnomad_exomes_ac": 209,
"gnomad_genomes_ac": 262,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6600000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.157,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_001199397.3",
"gene_symbol": "NEK1",
"hgnc_id": 7744,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1581T>C",
"hgvs_p": "p.Ala527Ala"
}
],
"clinvar_disease": "Connective tissue disorder,NEK1-related disorder,Short-rib thoracic dysplasia 6 with or without polydactyly,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"phenotype_combined": "Short-rib thoracic dysplasia 6 with or without polydactyly|Connective tissue disorder|NEK1-related disorder|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}