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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: 2-50497383-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=50497383&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 50497383,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000401669.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2829A>G",
"hgvs_p": "p.Leu943Leu",
"transcript": "NM_001330078.2",
"protein_id": "NP_001317007.1",
"transcript_support_level": null,
"aa_start": 943,
"aa_end": null,
"aa_length": 1507,
"cds_start": 2829,
"cds_end": null,
"cds_length": 4524,
"cdna_start": 3902,
"cdna_end": null,
"cdna_length": 9038,
"mane_select": "ENST00000401669.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2829A>G",
"hgvs_p": "p.Leu943Leu",
"transcript": "ENST00000401669.7",
"protein_id": "ENSP00000385017.2",
"transcript_support_level": 5,
"aa_start": 943,
"aa_end": null,
"aa_length": 1507,
"cds_start": 2829,
"cds_end": null,
"cds_length": 4524,
"cdna_start": 3902,
"cdna_end": null,
"cdna_length": 9038,
"mane_select": "NM_001330078.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2949A>G",
"hgvs_p": "p.Leu983Leu",
"transcript": "ENST00000404971.5",
"protein_id": "ENSP00000385142.1",
"transcript_support_level": 1,
"aa_start": 983,
"aa_end": null,
"aa_length": 1547,
"cds_start": 2949,
"cds_end": null,
"cds_length": 4644,
"cdna_start": 4289,
"cdna_end": null,
"cdna_length": 7578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2805A>G",
"hgvs_p": "p.Leu935Leu",
"transcript": "ENST00000625672.2",
"protein_id": "ENSP00000485887.1",
"transcript_support_level": 1,
"aa_start": 935,
"aa_end": null,
"aa_length": 1496,
"cds_start": 2805,
"cds_end": null,
"cds_length": 4491,
"cdna_start": 2988,
"cdna_end": null,
"cdna_length": 8113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2949A>G",
"hgvs_p": "p.Leu983Leu",
"transcript": "NM_001135659.3",
"protein_id": "NP_001129131.1",
"transcript_support_level": null,
"aa_start": 983,
"aa_end": null,
"aa_length": 1547,
"cds_start": 2949,
"cds_end": null,
"cds_length": 4644,
"cdna_start": 4022,
"cdna_end": null,
"cdna_length": 9158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2826A>G",
"hgvs_p": "p.Leu942Leu",
"transcript": "NM_001330093.2",
"protein_id": "NP_001317022.1",
"transcript_support_level": null,
"aa_start": 942,
"aa_end": null,
"aa_length": 1506,
"cds_start": 2826,
"cds_end": null,
"cds_length": 4521,
"cdna_start": 3899,
"cdna_end": null,
"cdna_length": 9035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2829A>G",
"hgvs_p": "p.Leu943Leu",
"transcript": "NM_001330086.2",
"protein_id": "NP_001317015.1",
"transcript_support_level": null,
"aa_start": 943,
"aa_end": null,
"aa_length": 1504,
"cds_start": 2829,
"cds_end": null,
"cds_length": 4515,
"cdna_start": 3902,
"cdna_end": null,
"cdna_length": 9029,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2817A>G",
"hgvs_p": "p.Leu939Leu",
"transcript": "NM_001330094.2",
"protein_id": "NP_001317023.1",
"transcript_support_level": null,
"aa_start": 939,
"aa_end": null,
"aa_length": 1500,
"cds_start": 2817,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 3890,
"cdna_end": null,
"cdna_length": 9017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2805A>G",
"hgvs_p": "p.Leu935Leu",
"transcript": "NM_001330077.2",
"protein_id": "NP_001317006.1",
"transcript_support_level": null,
"aa_start": 935,
"aa_end": null,
"aa_length": 1499,
"cds_start": 2805,
"cds_end": null,
"cds_length": 4500,
"cdna_start": 3878,
"cdna_end": null,
"cdna_length": 9014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2805A>G",
"hgvs_p": "p.Leu935Leu",
"transcript": "ENST00000630543.2",
"protein_id": "ENSP00000486879.1",
"transcript_support_level": 5,
"aa_start": 935,
"aa_end": null,
"aa_length": 1499,
"cds_start": 2805,
"cds_end": null,
"cds_length": 4500,
"cdna_start": 2805,
"cdna_end": null,
"cdna_length": 4500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2802A>G",
"hgvs_p": "p.Leu934Leu",
"transcript": "NM_001330085.2",
"protein_id": "NP_001317014.1",
"transcript_support_level": null,
"aa_start": 934,
"aa_end": null,
"aa_length": 1498,
"cds_start": 2802,
"cds_end": null,
"cds_length": 4497,
"cdna_start": 3875,
"cdna_end": null,
"cdna_length": 9011,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2805A>G",
"hgvs_p": "p.Leu935Leu",
"transcript": "NM_001330082.2",
"protein_id": "NP_001317011.1",
"transcript_support_level": null,
"aa_start": 935,
"aa_end": null,
"aa_length": 1496,
"cds_start": 2805,
"cds_end": null,
"cds_length": 4491,
"cdna_start": 3878,
"cdna_end": null,
"cdna_length": 9005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2793A>G",
"hgvs_p": "p.Leu931Leu",
"transcript": "ENST00000405472.7",
"protein_id": "ENSP00000434015.2",
"transcript_support_level": 5,
"aa_start": 931,
"aa_end": null,
"aa_length": 1495,
"cds_start": 2793,
"cds_end": null,
"cds_length": 4488,
"cdna_start": 3848,
"cdna_end": null,
"cdna_length": 5724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2763A>G",
"hgvs_p": "p.Leu921Leu",
"transcript": "NM_001330084.2",
"protein_id": "NP_001317013.1",
"transcript_support_level": null,
"aa_start": 921,
"aa_end": null,
"aa_length": 1485,
"cds_start": 2763,
"cds_end": null,
"cds_length": 4458,
"cdna_start": 3836,
"cdna_end": null,
"cdna_length": 8972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2829A>G",
"hgvs_p": "p.Leu943Leu",
"transcript": "NM_004801.6",
"protein_id": "NP_004792.1",
"transcript_support_level": null,
"aa_start": 943,
"aa_end": null,
"aa_length": 1477,
"cds_start": 2829,
"cds_end": null,
"cds_length": 4434,
"cdna_start": 3902,
"cdna_end": null,
"cdna_length": 8948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2829A>G",
"hgvs_p": "p.Leu943Leu",
"transcript": "ENST00000406316.6",
"protein_id": "ENSP00000384311.2",
"transcript_support_level": 5,
"aa_start": 943,
"aa_end": null,
"aa_length": 1477,
"cds_start": 2829,
"cds_end": null,
"cds_length": 4434,
"cdna_start": 4331,
"cdna_end": null,
"cdna_length": 9375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2778A>G",
"hgvs_p": "p.Leu926Leu",
"transcript": "NM_001330095.2",
"protein_id": "NP_001317024.1",
"transcript_support_level": null,
"aa_start": 926,
"aa_end": null,
"aa_length": 1460,
"cds_start": 2778,
"cds_end": null,
"cds_length": 4383,
"cdna_start": 3851,
"cdna_end": null,
"cdna_length": 8897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2763A>G",
"hgvs_p": "p.Leu921Leu",
"transcript": "NM_001330083.2",
"protein_id": "NP_001317012.1",
"transcript_support_level": null,
"aa_start": 921,
"aa_end": null,
"aa_length": 1452,
"cds_start": 2763,
"cds_end": null,
"cds_length": 4359,
"cdna_start": 3836,
"cdna_end": null,
"cdna_length": 8873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2748A>G",
"hgvs_p": "p.Leu916Leu",
"transcript": "NM_001330088.2",
"protein_id": "NP_001317017.1",
"transcript_support_level": null,
"aa_start": 916,
"aa_end": null,
"aa_length": 1447,
"cds_start": 2748,
"cds_end": null,
"cds_length": 4344,
"cdna_start": 3821,
"cdna_end": null,
"cdna_length": 8858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2718A>G",
"hgvs_p": "p.Leu906Leu",
"transcript": "NM_001330087.2",
"protein_id": "NP_001317016.1",
"transcript_support_level": null,
"aa_start": 906,
"aa_end": null,
"aa_length": 1440,
"cds_start": 2718,
"cds_end": null,
"cds_length": 4323,
"cdna_start": 3791,
"cdna_end": null,
"cdna_length": 8837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "c.2718A>G",
"hgvs_p": "p.Leu906Leu",
"transcript": "NM_001330096.2",
"protein_id": "NP_001317025.1",
"transcript_support_level": null,
"aa_start": 906,
"aa_end": null,
"aa_length": 1437,
"cds_start": 2718,
"cds_end": null,
"cds_length": 4314,
"cdna_start": 3791,
"cdna_end": null,
"cdna_length": 8828,
"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": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "n.1983A>G",
"hgvs_p": null,
"transcript": "ENST00000331040.9",
"protein_id": "ENSP00000489573.1",
"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": 3044,
"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,
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"transcript": "ENST00000462791.2",
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"transcript_support_level": 4,
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"cds_start": -4,
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
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"exon_count": 13,
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"gene_symbol": "NRXN1",
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"transcript": "ENST00000636298.1",
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},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
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"exon_count": 9,
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"gene_symbol": "NRXN1",
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"hgvs_c": "n.-5A>G",
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"transcript": "ENST00000637889.1",
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"transcript_support_level": 5,
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"cds_start": -4,
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"cdna_length": 2717,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
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"exon_count": 3,
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"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"hgvs_c": "n.*192A>G",
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"transcript": "ENST00000474354.1",
"protein_id": null,
"transcript_support_level": 4,
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"cds_start": -4,
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"cdna_length": 574,
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"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NRXN1",
"gene_hgnc_id": 8008,
"dbsnp": "rs754048752",
"frequency_reference_population": 0.00001471361,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000147136,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8799999952316284,
"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": -0.88,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.83,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000401669.7",
"gene_symbol": "NRXN1",
"hgnc_id": 8008,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.2829A>G",
"hgvs_p": "p.Leu943Leu"
}
],
"clinvar_disease": "Pitt-Hopkins-like syndrome 2",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Pitt-Hopkins-like syndrome 2",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}