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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: 13-52127646-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=52127646&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 52127646,
"ref": "T",
"alt": "C",
"effect": "5_prime_UTR_variant",
"transcript": "ENST00000684899.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-74A>G",
"hgvs_p": null,
"transcript": "NM_001365552.1",
"protein_id": "NP_001352481.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 832,
"cds_start": -4,
"cds_end": null,
"cds_length": 2499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5971,
"mane_select": "ENST00000684899.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-74A>G",
"hgvs_p": null,
"transcript": "ENST00000684899.1",
"protein_id": "ENSP00000509632.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 832,
"cds_start": -4,
"cds_end": null,
"cds_length": 2499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5971,
"mane_select": "NM_001365552.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-74A>G",
"hgvs_p": null,
"transcript": "ENST00000355568.8",
"protein_id": "ENSP00000347767.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 708,
"cds_start": -4,
"cds_end": null,
"cds_length": 2127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Lys48Arg",
"transcript": "XM_047430287.1",
"protein_id": "XP_047286243.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 904,
"cds_start": 143,
"cds_end": null,
"cds_length": 2715,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 6177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Lys48Arg",
"transcript": "XM_047430288.1",
"protein_id": "XP_047286244.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 903,
"cds_start": 143,
"cds_end": null,
"cds_length": 2712,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 6174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.98A>G",
"hgvs_p": "p.Lys33Arg",
"transcript": "XM_047430289.1",
"protein_id": "XP_047286245.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 889,
"cds_start": 98,
"cds_end": null,
"cds_length": 2670,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 6464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Lys48Arg",
"transcript": "XM_047430290.1",
"protein_id": "XP_047286246.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 881,
"cds_start": 143,
"cds_end": null,
"cds_length": 2646,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 6108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Lys48Arg",
"transcript": "XM_047430291.1",
"protein_id": "XP_047286247.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 873,
"cds_start": 143,
"cds_end": null,
"cds_length": 2622,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 6084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Lys48Arg",
"transcript": "XM_017020556.2",
"protein_id": "XP_016876045.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 737,
"cds_start": 143,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Lys48Arg",
"transcript": "XM_011535066.3",
"protein_id": "XP_011533368.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 697,
"cds_start": 143,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3155,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Lys48Arg",
"transcript": "XM_006719808.5",
"protein_id": "XP_006719871.2",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 598,
"cds_start": 143,
"cds_end": null,
"cds_length": 1797,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 2015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Lys48Arg",
"transcript": "XM_011535068.3",
"protein_id": "XP_011533370.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 483,
"cds_start": 143,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 1792,
"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": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "n.268A>G",
"hgvs_p": null,
"transcript": "XR_941574.3",
"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": 3154,
"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": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "n.268A>G",
"hgvs_p": null,
"transcript": "XR_941575.3",
"protein_id": null,
"transcript_support_level": null,
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"aa_end": null,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-74A>G",
"hgvs_p": null,
"transcript": "ENST00000647945.2",
"protein_id": "ENSP00000497892.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 857,
"cds_start": -4,
"cds_end": null,
"cds_length": 2574,
"cdna_start": null,
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"cdna_length": 6051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-74A>G",
"hgvs_p": null,
"transcript": "NM_199289.3",
"protein_id": "NP_954983.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-74A>G",
"hgvs_p": null,
"transcript": "XM_047430293.1",
"protein_id": "XP_047286249.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 790,
"cds_start": -4,
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"cds_length": 2373,
"cdna_start": null,
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"cdna_length": 5845,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-22-142A>G",
"hgvs_p": null,
"transcript": "ENST00000652119.1",
"protein_id": "ENSP00000498918.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 683,
"cds_start": -4,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
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"cdna_length": 2196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "n.64+1383A>G",
"hgvs_p": null,
"transcript": "ENST00000652502.1",
"protein_id": null,
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"aa_start": null,
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"cdna_start": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-22-142A>G",
"hgvs_p": null,
"transcript": "XM_047430292.1",
"protein_id": "XP_047286248.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 832,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-164A>G",
"hgvs_p": null,
"transcript": "ENST00000617045.1",
"protein_id": "ENSP00000477810.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "n.-164A>G",
"hgvs_p": null,
"transcript": "ENST00000465811.7",
"protein_id": "ENSP00000431956.2",
"transcript_support_level": 5,
"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": 1864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK5",
"gene_hgnc_id": 7748,
"hgvs_c": "c.-304A>G",
"hgvs_p": null,
"transcript": "XM_047430294.1",
"protein_id": "XP_047286250.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 753,
"cds_start": -4,
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"cds_length": 2262,
"cdna_start": null,
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}
],
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"gnomad_genomes_ac": 86494,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9100000262260437,
"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": -0.91,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.236,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000684899.1",
"gene_symbol": "NEK5",
"hgnc_id": 7748,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-74A>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}