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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: 9-37015163-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=37015163&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 37015163,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000358127.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "NM_016734.3",
"protein_id": "NP_057953.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 391,
"cds_start": 244,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8704,
"mane_select": "ENST00000358127.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "ENST00000358127.9",
"protein_id": "ENSP00000350844.4",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 391,
"cds_start": 244,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8704,
"mane_select": "NM_016734.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "ENST00000377853.6",
"protein_id": "ENSP00000367084.2",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 362,
"cds_start": 244,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 254,
"cdna_end": null,
"cdna_length": 1487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "ENST00000377852.7",
"protein_id": "ENSP00000367083.2",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 357,
"cds_start": 244,
"cds_end": null,
"cds_length": 1074,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "ENST00000414447.5",
"protein_id": "ENSP00000412188.1",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 348,
"cds_start": 244,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 244,
"cdna_end": null,
"cdna_length": 1056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "ENST00000377847.6",
"protein_id": "ENSP00000367078.2",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 328,
"cds_start": 244,
"cds_end": null,
"cds_length": 987,
"cdna_start": 244,
"cdna_end": null,
"cdna_length": 996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "ENST00000523241.6",
"protein_id": "ENSP00000429637.1",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 324,
"cds_start": 244,
"cds_end": null,
"cds_length": 975,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "ENST00000520281.5",
"protein_id": "ENSP00000430773.1",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 319,
"cds_start": 244,
"cds_end": null,
"cds_length": 960,
"cdna_start": 244,
"cdna_end": null,
"cdna_length": 969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "ENST00000520154.6",
"protein_id": "ENSP00000429291.1",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 295,
"cds_start": 244,
"cds_end": null,
"cds_length": 888,
"cdna_start": 398,
"cdna_end": null,
"cdna_length": 1399,
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "n.244G>A",
"hgvs_p": null,
"transcript": "ENST00000377840.6",
"protein_id": "ENSP00000367071.2",
"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": 1444,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "n.244G>A",
"hgvs_p": null,
"transcript": "ENST00000523493.5",
"protein_id": "ENSP00000431038.1",
"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": 1112,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.-81G>A",
"hgvs_p": null,
"transcript": "ENST00000522003.5",
"protein_id": "ENSP00000429359.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 283,
"cds_start": -4,
"cds_end": null,
"cds_length": 852,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1019,
"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": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.-81G>A",
"hgvs_p": null,
"transcript": "ENST00000523145.5",
"protein_id": "ENSP00000429197.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 220,
"cds_start": -4,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 830,
"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": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.212+5473G>A",
"hgvs_p": null,
"transcript": "ENST00000446742.5",
"protein_id": "ENSP00000404687.1",
"transcript_support_level": 1,
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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": "V",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "NM_001280548.2",
"protein_id": "NP_001267477.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 362,
"cds_start": 244,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8617,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "NM_001280547.2",
"protein_id": "NP_001267476.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 357,
"cds_start": 244,
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"cdna_start": 481,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "NM_001280554.2",
"protein_id": "NP_001267483.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 348,
"cds_start": 244,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "NM_001280552.2",
"protein_id": "NP_001267481.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 328,
"cds_start": 244,
"cds_end": null,
"cds_length": 987,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "NM_001280549.2",
"protein_id": "NP_001267478.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 324,
"cds_start": 244,
"cds_end": null,
"cds_length": 975,
"cdna_start": 481,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "NM_001280553.2",
"protein_id": "NP_001267482.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 319,
"cds_start": 244,
"cds_end": null,
"cds_length": 960,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile",
"transcript": "NM_001280550.2",
"protein_id": "NP_001267479.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 295,
"cds_start": 244,
"cds_end": null,
"cds_length": 888,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 8385,
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "n.481G>A",
"hgvs_p": null,
"transcript": "NR_103999.2",
"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": 8574,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"hgvs_c": "n.481G>A",
"hgvs_p": null,
"transcript": "NR_104000.2",
"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,
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
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],
"exon_rank": 2,
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"exon_count": 9,
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},
{
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"protein_coding": true,
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"exon_rank": 3,
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"exon_count": 10,
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"transcript": "ENST00000651550.1",
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"feature": null
},
{
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"protein_coding": true,
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"feature": null
},
{
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"strand": false,
"consequences": [
"intron_variant"
],
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"gene_symbol": "PAX5",
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},
{
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"intron_variant"
],
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"gene_symbol": "PAX5",
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"hgvs_c": "n.209+5473G>A",
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"transcript": "ENST00000651199.1",
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"feature": null
}
],
"gene_symbol": "PAX5",
"gene_hgnc_id": 8619,
"dbsnp": "rs587778589",
"frequency_reference_population": 0.0001623272,
"hom_count_reference_population": 0,
"allele_count_reference_population": 262,
"gnomad_exomes_af": 0.000168282,
"gnomad_genomes_af": 0.00010513,
"gnomad_exomes_ac": 246,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.017112374305725098,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.672,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4406,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BS1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 16,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000358127.9",
"gene_symbol": "PAX5",
"hgnc_id": 8619,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Val82Ile"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2 O:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}