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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: 4-142086239-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=142086239&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 142086239,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001101669.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001101669.3",
"protein_id": "NP_001095139.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2738,
"cdna_end": null,
"cdna_length": 8743,
"mane_select": "ENST00000262992.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "ENST00000262992.9",
"protein_id": "ENSP00000262992.4",
"transcript_support_level": 5,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2738,
"cdna_end": null,
"cdna_length": 8743,
"mane_select": "NM_001101669.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "ENST00000508116.5",
"protein_id": "ENSP00000423954.1",
"transcript_support_level": 1,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2745,
"cdna_end": null,
"cdna_length": 3165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "ENST00000513000.5",
"protein_id": "ENSP00000425487.1",
"transcript_support_level": 1,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2826,
"cdna_end": null,
"cdna_length": 8831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "ENST00000510812.5",
"protein_id": "ENSP00000427250.1",
"transcript_support_level": 1,
"aa_start": 798,
"aa_end": null,
"aa_length": 816,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2452,
"cdna_start": 2795,
"cdna_end": null,
"cdna_length": 2855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001331040.1",
"protein_id": "NP_001317969.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 938,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2817,
"cdna_start": 2972,
"cdna_end": null,
"cdna_length": 4569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385335.1",
"protein_id": "NP_001372264.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 938,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2817,
"cdna_start": 2675,
"cdna_end": null,
"cdna_length": 4272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "ENST00000509777.5",
"protein_id": "ENSP00000422793.1",
"transcript_support_level": 5,
"aa_start": 798,
"aa_end": null,
"aa_length": 938,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2817,
"cdna_start": 2737,
"cdna_end": null,
"cdna_length": 4334,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2419G>A",
"hgvs_p": "p.Glu807Lys",
"transcript": "NM_001385339.1",
"protein_id": "NP_001372268.1",
"transcript_support_level": null,
"aa_start": 807,
"aa_end": null,
"aa_length": 933,
"cds_start": 2419,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2908,
"cdna_end": null,
"cdna_length": 8913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2419G>A",
"hgvs_p": "p.Glu807Lys",
"transcript": "NM_001385343.1",
"protein_id": "NP_001372272.1",
"transcript_support_level": null,
"aa_start": 807,
"aa_end": null,
"aa_length": 933,
"cds_start": 2419,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2805,
"cdna_end": null,
"cdna_length": 8810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385334.1",
"protein_id": "NP_001372263.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2843,
"cdna_end": null,
"cdna_length": 8848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385336.1",
"protein_id": "NP_001372265.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
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"cds_length": 2775,
"cdna_start": 2901,
"cdna_end": null,
"cdna_length": 8906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385338.1",
"protein_id": "NP_001372267.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 2881,
"cdna_end": null,
"cdna_length": 8886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
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"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385341.1",
"protein_id": "NP_001372270.1",
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"aa_start": 798,
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"cds_start": 2392,
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"cdna_start": 2778,
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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": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385342.1",
"protein_id": "NP_001372271.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
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"cdna_start": 2714,
"cdna_end": null,
"cdna_length": 8719,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385344.1",
"protein_id": "NP_001372273.1",
"transcript_support_level": null,
"aa_start": 798,
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"cdna_start": 2942,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_003866.3",
"protein_id": "NP_003857.2",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 924,
"cds_start": 2392,
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"cdna_start": 3071,
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"cdna_length": 9076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385347.1",
"protein_id": "NP_001372276.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 920,
"cds_start": 2392,
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"cdna_start": 2778,
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"mane_select": null,
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"feature": null
},
{
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"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": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys",
"transcript": "NM_001385348.1",
"protein_id": "NP_001372277.1",
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"biotype": null,
"feature": null
},
{
"aa_ref": "E",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "NM_001385460.1",
"protein_id": "NP_001372389.1",
"transcript_support_level": null,
"aa_start": 669,
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"aa_length": 809,
"cds_start": 2005,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
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"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.1987G>A",
"hgvs_p": "p.Glu663Lys",
"transcript": "NM_001385351.1",
"protein_id": "NP_001372280.1",
"transcript_support_level": null,
"aa_start": 663,
"aa_end": null,
"aa_length": 789,
"cds_start": 1987,
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"cds_length": 2370,
"cdna_start": 2528,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"hgvs_c": "c.1837G>A",
"hgvs_p": "p.Glu613Lys",
"transcript": "NM_001385459.1",
"protein_id": "NP_001372388.1",
"transcript_support_level": null,
"aa_start": 613,
"aa_end": null,
"aa_length": 753,
"cds_start": 1837,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2037,
"cdna_end": null,
"cdna_length": 3634,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
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"hgvs_p": null,
"transcript": "ENST00000512630.5",
"protein_id": "ENSP00000423771.1",
"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": 2953,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "INPP4B",
"gene_hgnc_id": 6075,
"dbsnp": "rs139268004",
"frequency_reference_population": 0.00012265274,
"hom_count_reference_population": 0,
"allele_count_reference_population": 191,
"gnomad_exomes_af": 0.000130229,
"gnomad_genomes_af": 0.0000526247,
"gnomad_exomes_ac": 183,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1486620008945465,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.078,
"revel_prediction": "Benign",
"alphamissense_score": 0.1357,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.68,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001101669.3",
"gene_symbol": "INPP4B",
"hgnc_id": 6075,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Glu798Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}