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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: 1-5873220-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=5873220&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 5873220,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000378156.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "NM_015102.5",
"protein_id": "NP_055917.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1426,
"cds_start": -4,
"cds_end": null,
"cds_length": 4281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4955,
"mane_select": "ENST00000378156.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "ENST00000378156.9",
"protein_id": "ENSP00000367398.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1426,
"cds_start": -4,
"cds_end": null,
"cds_length": 4281,
"cdna_start": null,
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*2216+32G>A",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*1126+32G>A",
"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": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1779+32G>A",
"hgvs_p": null,
"transcript": "NM_001291594.2",
"protein_id": "NP_001278523.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 914,
"cds_start": -4,
"cds_end": null,
"cds_length": 2745,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1776+32G>A",
"hgvs_p": null,
"transcript": "NM_001291593.2",
"protein_id": "NP_001278522.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 913,
"cds_start": -4,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.590+32G>A",
"hgvs_p": null,
"transcript": "ENST00000468253.1",
"protein_id": null,
"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": 781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.3047+32G>A",
"hgvs_p": null,
"transcript": "ENST00000478423.6",
"protein_id": null,
"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": 4467,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.4082+32G>A",
"hgvs_p": null,
"transcript": "NR_111987.2",
"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": 5502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "XM_006710563.4",
"protein_id": "XP_006710626.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1426,
"cds_start": -4,
"cds_end": null,
"cds_length": 4281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "XM_011541216.3",
"protein_id": "XP_011539518.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1426,
"cds_start": -4,
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"cds_length": 4281,
"cdna_start": null,
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"cdna_length": 5493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "XM_011541217.3",
"protein_id": "XP_011539519.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1426,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 5357,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "XM_047417535.1",
"protein_id": "XP_047273491.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1426,
"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
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 31,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "XM_047417537.1",
"protein_id": "XP_047273493.1",
"transcript_support_level": null,
"aa_start": null,
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 31,
"intron_rank": 24,
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"gene_symbol": "NPHP4",
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"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "XM_047417538.1",
"protein_id": "XP_047273494.1",
"transcript_support_level": null,
"aa_start": null,
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"cdna_start": null,
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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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3315+32G>A",
"hgvs_p": null,
"transcript": "XM_047417546.1",
"protein_id": "XP_047273502.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 29,
"intron_rank": 22,
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"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3312+32G>A",
"hgvs_p": null,
"transcript": "XM_011541213.2",
"protein_id": "XP_011539515.1",
"transcript_support_level": null,
"aa_start": null,
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"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
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3273+32G>A",
"hgvs_p": null,
"transcript": "XM_011541214.2",
"protein_id": "XP_011539516.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1412,
"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
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3270+32G>A",
"hgvs_p": null,
"transcript": "XM_017000996.2",
"protein_id": "XP_016856485.1",
"transcript_support_level": null,
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 21,
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"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3204+32G>A",
"hgvs_p": null,
"transcript": "XM_011541215.2",
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 20,
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"gene_symbol": "NPHP4",
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"hgvs_c": "c.2973+32G>A",
"hgvs_p": null,
"transcript": "XM_047417555.1",
"protein_id": "XP_047273511.1",
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},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2970+32G>A",
"hgvs_p": null,
"transcript": "XM_047417565.1",
"protein_id": "XP_047273521.1",
"transcript_support_level": null,
"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
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2787+32G>A",
"hgvs_p": null,
"transcript": "XM_017000999.2",
"protein_id": "XP_016856488.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1250,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
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],
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"splice_prediction_selected": "Benign",
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"bayesdelnoaf_score": -0.95,
"bayesdelnoaf_prediction": "Benign",
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"phylop100way_prediction": "Benign",
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"spliceai_max_prediction": "Benign",
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"acmg_score": -20,
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"acmg_by_gene": [
{
"score": -20,
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"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
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],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}