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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: 1-5864497-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=5864497&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 5864497,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000378156.9",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "NM_015102.5",
"protein_id": "NP_055917.1",
"transcript_support_level": null,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4057,
"cdna_end": null,
"cdna_length": 4955,
"mane_select": "ENST00000378156.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "ENST00000378156.9",
"protein_id": "ENSP00000367398.4",
"transcript_support_level": 1,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4057,
"cdna_end": null,
"cdna_length": 4955,
"mane_select": "NM_015102.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*2738C>T",
"hgvs_p": null,
"transcript": "ENST00000378169.7",
"protein_id": "ENSP00000367411.3",
"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": 4213,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.2585C>T",
"hgvs_p": null,
"transcript": "ENST00000460696.1",
"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": 3967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*1648C>T",
"hgvs_p": null,
"transcript": "ENST00000489180.6",
"protein_id": "ENSP00000423747.1",
"transcript_support_level": 2,
"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": 5548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*2738C>T",
"hgvs_p": null,
"transcript": "ENST00000378169.7",
"protein_id": "ENSP00000367411.3",
"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": 4213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*1648C>T",
"hgvs_p": null,
"transcript": "ENST00000489180.6",
"protein_id": "ENSP00000423747.1",
"transcript_support_level": 2,
"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": 5548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3665C>T",
"hgvs_p": "p.Ser1222Leu",
"transcript": "XM_047417574.1",
"protein_id": "XP_047273530.1",
"transcript_support_level": null,
"aa_start": 1222,
"aa_end": null,
"aa_length": 1235,
"cds_start": 3665,
"cds_end": null,
"cds_length": 3708,
"cdna_start": 3703,
"cdna_end": null,
"cdna_length": 3846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2301C>T",
"hgvs_p": "p.Phe767Phe",
"transcript": "NM_001291594.2",
"protein_id": "NP_001278523.1",
"transcript_support_level": null,
"aa_start": 767,
"aa_end": null,
"aa_length": 914,
"cds_start": 2301,
"cds_end": null,
"cds_length": 2745,
"cdna_start": 3570,
"cdna_end": null,
"cdna_length": 4468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2298C>T",
"hgvs_p": "p.Phe766Phe",
"transcript": "NM_001291593.2",
"protein_id": "NP_001278522.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 913,
"cds_start": 2298,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 3747,
"cdna_end": null,
"cdna_length": 4645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "XM_006710563.4",
"protein_id": "XP_006710626.1",
"transcript_support_level": null,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4044,
"cdna_end": null,
"cdna_length": 4942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "XM_011541216.3",
"protein_id": "XP_011539518.1",
"transcript_support_level": null,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4595,
"cdna_end": null,
"cdna_length": 5493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "XM_011541217.3",
"protein_id": "XP_011539519.1",
"transcript_support_level": null,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4459,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "XM_047417535.1",
"protein_id": "XP_047273491.1",
"transcript_support_level": null,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4584,
"cdna_end": null,
"cdna_length": 5482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "XM_047417537.1",
"protein_id": "XP_047273493.1",
"transcript_support_level": null,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4193,
"cdna_end": null,
"cdna_length": 5091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "XM_047417538.1",
"protein_id": "XP_047273494.1",
"transcript_support_level": null,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4493,
"cdna_end": null,
"cdna_length": 5391,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3837C>T",
"hgvs_p": "p.Phe1279Phe",
"transcript": "XM_047417546.1",
"protein_id": "XP_047273502.1",
"transcript_support_level": null,
"aa_start": 1279,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3837,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4357,
"cdna_end": null,
"cdna_length": 5255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3834C>T",
"hgvs_p": "p.Phe1278Phe",
"transcript": "XM_011541213.2",
"protein_id": "XP_011539515.1",
"transcript_support_level": null,
"aa_start": 1278,
"aa_end": null,
"aa_length": 1425,
"cds_start": 3834,
"cds_end": null,
"cds_length": 4278,
"cdna_start": 3872,
"cdna_end": null,
"cdna_length": 4770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3795C>T",
"hgvs_p": "p.Phe1265Phe",
"transcript": "XM_011541214.2",
"protein_id": "XP_011539516.1",
"transcript_support_level": null,
"aa_start": 1265,
"aa_end": null,
"aa_length": 1412,
"cds_start": 3795,
"cds_end": null,
"cds_length": 4239,
"cdna_start": 3833,
"cdna_end": null,
"cdna_length": 4731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3792C>T",
"hgvs_p": "p.Phe1264Phe",
"transcript": "XM_017000996.2",
"protein_id": "XP_016856485.1",
"transcript_support_level": null,
"aa_start": 1264,
"aa_end": null,
"aa_length": 1411,
"cds_start": 3792,
"cds_end": null,
"cds_length": 4236,
"cdna_start": 3830,
"cdna_end": null,
"cdna_length": 4728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3726C>T",
"hgvs_p": "p.Phe1242Phe",
"transcript": "XM_011541215.2",
"protein_id": "XP_011539517.1",
"transcript_support_level": null,
"aa_start": 1242,
"aa_end": null,
"aa_length": 1389,
"cds_start": 3726,
"cds_end": null,
"cds_length": 4170,
"cdna_start": 3764,
"cdna_end": null,
"cdna_length": 4662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3495C>T",
"hgvs_p": "p.Phe1165Phe",
"transcript": "XM_047417555.1",
"protein_id": "XP_047273511.1",
"transcript_support_level": null,
"aa_start": 1165,
"aa_end": null,
"aa_length": 1312,
"cds_start": 3495,
"cds_end": null,
"cds_length": 3939,
"cdna_start": 3533,
"cdna_end": null,
"cdna_length": 4431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
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],
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"splice_prediction_selected": "Benign",
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"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.72,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.18,
"spliceai_max_prediction": "Benign",
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"acmg_score": -10,
"acmg_classification": "Benign",
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"acmg_by_gene": [
{
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"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
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"BP6",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000378156.9",
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],
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],
"clinvar_disease": "NPHP4-related disorder,Nephronophthisis,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not provided|Nephronophthisis|NPHP4-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}