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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: 1-5967324-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=5967324&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 5967324,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_015102.5",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "NM_015102.5",
"protein_id": "NP_055917.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1426,
"cds_start": 492,
"cds_end": null,
"cds_length": 4281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000378156.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015102.5"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000378156.9",
"protein_id": "ENSP00000367398.4",
"transcript_support_level": 1,
"aa_start": 164,
"aa_end": null,
"aa_length": 1426,
"cds_start": 492,
"cds_end": null,
"cds_length": 4281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015102.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378156.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.492C>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": 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": "ENST00000378169.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.492C>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": 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": "ENST00000489180.6"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000923561.1",
"protein_id": "ENSP00000593620.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1426,
"cds_start": 492,
"cds_end": null,
"cds_length": 4281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923561.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000923565.1",
"protein_id": "ENSP00000593624.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1426,
"cds_start": 492,
"cds_end": null,
"cds_length": 4281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923565.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000892397.1",
"protein_id": "ENSP00000562456.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1425,
"cds_start": 492,
"cds_end": null,
"cds_length": 4278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892397.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000892402.1",
"protein_id": "ENSP00000562461.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1425,
"cds_start": 492,
"cds_end": null,
"cds_length": 4278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892402.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000923562.1",
"protein_id": "ENSP00000593621.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1425,
"cds_start": 492,
"cds_end": null,
"cds_length": 4278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923562.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000923564.1",
"protein_id": "ENSP00000593623.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1425,
"cds_start": 492,
"cds_end": null,
"cds_length": 4278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923564.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000955275.1",
"protein_id": "ENSP00000625334.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1425,
"cds_start": 492,
"cds_end": null,
"cds_length": 4278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955275.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000955267.1",
"protein_id": "ENSP00000625326.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1423,
"cds_start": 492,
"cds_end": null,
"cds_length": 4272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955267.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000955271.1",
"protein_id": "ENSP00000625330.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1422,
"cds_start": 492,
"cds_end": null,
"cds_length": 4269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955271.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.480C>T",
"hgvs_p": "p.His160His",
"transcript": "ENST00000955273.1",
"protein_id": "ENSP00000625332.1",
"transcript_support_level": null,
"aa_start": 160,
"aa_end": null,
"aa_length": 1421,
"cds_start": 480,
"cds_end": null,
"cds_length": 4266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955273.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000955266.1",
"protein_id": "ENSP00000625325.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1412,
"cds_start": 492,
"cds_end": null,
"cds_length": 4239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955266.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000892399.1",
"protein_id": "ENSP00000562458.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1411,
"cds_start": 492,
"cds_end": null,
"cds_length": 4236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892399.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000955269.1",
"protein_id": "ENSP00000625328.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1411,
"cds_start": 492,
"cds_end": null,
"cds_length": 4236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955269.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000892395.1",
"protein_id": "ENSP00000562454.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1390,
"cds_start": 492,
"cds_end": null,
"cds_length": 4173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892395.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000955272.1",
"protein_id": "ENSP00000625331.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1390,
"cds_start": 492,
"cds_end": null,
"cds_length": 4173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955272.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000955268.1",
"protein_id": "ENSP00000625327.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1389,
"cds_start": 492,
"cds_end": null,
"cds_length": 4170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955268.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.492C>T",
"hgvs_p": "p.His164His",
"transcript": "ENST00000955274.1",
"protein_id": "ENSP00000625333.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1389,
"cds_start": 492,
"cds_end": null,
"cds_length": 4170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955274.1"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.348C>T",
"hgvs_p": "p.His116His",
"transcript": "ENST00000892400.1",
"protein_id": "ENSP00000562459.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 1378,
"cds_start": 348,
"cds_end": null,
"cds_length": 4137,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892400.1"
},
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],
"gene_symbol": "NPHP4",
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"computational_score_selected": -0.4300000071525574,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.188,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"spliceai_max_prediction": "Benign",
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"mitotip_prediction": null,
"acmg_score": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
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"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_015102.5",
"gene_symbol": "NPHP4",
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"effects": [
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],
"inheritance_mode": "AR",
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"hgvs_p": "p.His164His"
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],
"clinvar_disease": "Nephronophthisis",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Nephronophthisis",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}