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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: 5-78039191-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=78039191&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 78039191,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000255194.11",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2661C>A",
"hgvs_p": "p.Phe887Leu",
"transcript": "NM_003664.5",
"protein_id": "NP_003655.3",
"transcript_support_level": null,
"aa_start": 887,
"aa_end": null,
"aa_length": 1094,
"cds_start": 2661,
"cds_end": null,
"cds_length": 3285,
"cdna_start": 2780,
"cdna_end": null,
"cdna_length": 3980,
"mane_select": "ENST00000255194.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2661C>A",
"hgvs_p": "p.Phe887Leu",
"transcript": "ENST00000255194.11",
"protein_id": "ENSP00000255194.7",
"transcript_support_level": 1,
"aa_start": 887,
"aa_end": null,
"aa_length": 1094,
"cds_start": 2661,
"cds_end": null,
"cds_length": 3285,
"cdna_start": 2780,
"cdna_end": null,
"cdna_length": 3980,
"mane_select": "NM_003664.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2514C>A",
"hgvs_p": "p.Phe838Leu",
"transcript": "ENST00000519295.7",
"protein_id": "ENSP00000430597.1",
"transcript_support_level": 1,
"aa_start": 838,
"aa_end": null,
"aa_length": 1045,
"cds_start": 2514,
"cds_end": null,
"cds_length": 3138,
"cdna_start": 2828,
"cdna_end": null,
"cdna_length": 14714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2661C>A",
"hgvs_p": "p.Phe887Leu",
"transcript": "ENST00000695515.1",
"protein_id": "ENSP00000511978.1",
"transcript_support_level": null,
"aa_start": 887,
"aa_end": null,
"aa_length": 1055,
"cds_start": 2661,
"cds_end": null,
"cds_length": 3168,
"cdna_start": 2661,
"cdna_end": null,
"cdna_length": 3744,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2661C>A",
"hgvs_p": "p.Phe887Leu",
"transcript": "ENST00000695511.1",
"protein_id": "ENSP00000511974.1",
"transcript_support_level": null,
"aa_start": 887,
"aa_end": null,
"aa_length": 1053,
"cds_start": 2661,
"cds_end": null,
"cds_length": 3162,
"cdna_start": 2819,
"cdna_end": null,
"cdna_length": 4045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2655C>A",
"hgvs_p": "p.Phe885Leu",
"transcript": "ENST00000695454.1",
"protein_id": "ENSP00000511922.1",
"transcript_support_level": null,
"aa_start": 885,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2655,
"cds_end": null,
"cds_length": 3156,
"cdna_start": 2838,
"cdna_end": null,
"cdna_length": 4064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2526C>A",
"hgvs_p": "p.Phe842Leu",
"transcript": "ENST00000695513.1",
"protein_id": "ENSP00000511976.1",
"transcript_support_level": null,
"aa_start": 842,
"aa_end": null,
"aa_length": 1049,
"cds_start": 2526,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 2786,
"cdna_end": null,
"cdna_length": 3973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2514C>A",
"hgvs_p": "p.Phe838Leu",
"transcript": "NM_001271769.2",
"protein_id": "NP_001258698.1",
"transcript_support_level": null,
"aa_start": 838,
"aa_end": null,
"aa_length": 1045,
"cds_start": 2514,
"cds_end": null,
"cds_length": 3138,
"cdna_start": 2792,
"cdna_end": null,
"cdna_length": 5796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2604C>A",
"hgvs_p": "p.Phe868Leu",
"transcript": "ENST00000695453.1",
"protein_id": "ENSP00000511921.1",
"transcript_support_level": null,
"aa_start": 868,
"aa_end": null,
"aa_length": 1034,
"cds_start": 2604,
"cds_end": null,
"cds_length": 3105,
"cdna_start": 2751,
"cdna_end": null,
"cdna_length": 3977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2481C>A",
"hgvs_p": "p.Phe827Leu",
"transcript": "ENST00000695512.1",
"protein_id": "ENSP00000511975.1",
"transcript_support_level": null,
"aa_start": 827,
"aa_end": null,
"aa_length": 1034,
"cds_start": 2481,
"cds_end": null,
"cds_length": 3105,
"cdna_start": 2639,
"cdna_end": null,
"cdna_length": 3794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2661C>A",
"hgvs_p": "p.Phe887Leu",
"transcript": "ENST00000695510.1",
"protein_id": "ENSP00000511973.1",
"transcript_support_level": null,
"aa_start": 887,
"aa_end": null,
"aa_length": 1008,
"cds_start": 2661,
"cds_end": null,
"cds_length": 3027,
"cdna_start": 2819,
"cdna_end": null,
"cdna_length": 3833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2514C>A",
"hgvs_p": "p.Phe838Leu",
"transcript": "ENST00000695455.1",
"protein_id": "ENSP00000511923.1",
"transcript_support_level": null,
"aa_start": 838,
"aa_end": null,
"aa_length": 1004,
"cds_start": 2514,
"cds_end": null,
"cds_length": 3015,
"cdna_start": 2789,
"cdna_end": null,
"cdna_length": 4015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1860C>A",
"hgvs_p": "p.Phe620Leu",
"transcript": "ENST00000695450.1",
"protein_id": "ENSP00000511919.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 827,
"cds_start": 1860,
"cds_end": null,
"cds_length": 2484,
"cdna_start": 1905,
"cdna_end": null,
"cdna_length": 3090,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.461C>A",
"hgvs_p": null,
"transcript": "ENST00000523204.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 1661,
"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": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.2554C>A",
"hgvs_p": null,
"transcript": "ENST00000695447.1",
"protein_id": "ENSP00000511917.1",
"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": 3175,
"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": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.*2423C>A",
"hgvs_p": null,
"transcript": "ENST00000695451.1",
"protein_id": "ENSP00000511920.1",
"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": 4175,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.376C>A",
"hgvs_p": null,
"transcript": "ENST00000695458.1",
"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": 3921,
"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": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.2661C>A",
"hgvs_p": null,
"transcript": "ENST00000695488.1",
"protein_id": "ENSP00000511959.1",
"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": 4042,
"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": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.2819C>A",
"hgvs_p": null,
"transcript": "ENST00000695505.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 4765,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.313C>A",
"hgvs_p": null,
"transcript": "ENST00000695506.1",
"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": 1488,
"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": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.*186C>A",
"hgvs_p": null,
"transcript": "ENST00000695507.1",
"protein_id": "ENSP00000511970.1",
"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": 4108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.*2423C>A",
"hgvs_p": null,
"transcript": "ENST00000695451.1",
"protein_id": "ENSP00000511920.1",
"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": 4175,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.*186C>A",
"hgvs_p": null,
"transcript": "ENST00000695507.1",
"protein_id": "ENSP00000511970.1",
"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": 4108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.-43C>A",
"hgvs_p": null,
"transcript": "ENST00000522901.1",
"protein_id": "ENSP00000429228.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": -4,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"dbsnp": "rs139344924",
"frequency_reference_population": 0.010180375,
"hom_count_reference_population": 110,
"allele_count_reference_population": 16432,
"gnomad_exomes_af": 0.0105184,
"gnomad_genomes_af": 0.00693551,
"gnomad_exomes_ac": 15376,
"gnomad_genomes_ac": 1056,
"gnomad_exomes_homalt": 105,
"gnomad_genomes_homalt": 5,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011465996503829956,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.059,
"revel_prediction": "Benign",
"alphamissense_score": 0.3009,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.631,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000255194.11",
"gene_symbol": "AP3B1",
"hgnc_id": 566,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2661C>A",
"hgvs_p": "p.Phe887Leu"
}
],
"clinvar_disease": "Autoinflammatory syndrome,Hermansky-Pudlak syndrome,Hermansky-Pudlak syndrome 2,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:5",
"phenotype_combined": "not specified|Hermansky-Pudlak syndrome 2|Hermansky-Pudlak syndrome|not provided|Autoinflammatory syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}