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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: 6-83188678-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=83188678&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 83188678,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000513973.6",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "NM_015599.3",
"protein_id": "NP_056414.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 542,
"cds_start": 325,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 414,
"cdna_end": null,
"cdna_length": 6079,
"mane_select": "ENST00000513973.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000513973.6",
"protein_id": "ENSP00000424874.1",
"transcript_support_level": 1,
"aa_start": 109,
"aa_end": null,
"aa_length": 542,
"cds_start": 325,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 414,
"cdna_end": null,
"cdna_length": 6079,
"mane_select": "NM_015599.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000512866.5",
"protein_id": "ENSP00000421565.1",
"transcript_support_level": 1,
"aa_start": 109,
"aa_end": null,
"aa_length": 566,
"cds_start": 325,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 380,
"cdna_end": null,
"cdna_length": 2013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.82A>T",
"hgvs_p": "p.Ile28Phe",
"transcript": "ENST00000283977.9",
"protein_id": "ENSP00000283977.5",
"transcript_support_level": 5,
"aa_start": 28,
"aa_end": null,
"aa_length": 441,
"cds_start": 82,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 2223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.409A>T",
"hgvs_p": "p.Ile137Phe",
"transcript": "NM_001199917.2",
"protein_id": "NP_001186846.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 570,
"cds_start": 409,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 6207,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.409A>T",
"hgvs_p": "p.Ile137Phe",
"transcript": "NM_001367287.1",
"protein_id": "NP_001354216.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 570,
"cds_start": 409,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 551,
"cdna_end": null,
"cdna_length": 6216,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.409A>T",
"hgvs_p": "p.Ile137Phe",
"transcript": "ENST00000506587.5",
"protein_id": "ENSP00000425809.1",
"transcript_support_level": 2,
"aa_start": 137,
"aa_end": null,
"aa_length": 570,
"cds_start": 409,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 1971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.409A>T",
"hgvs_p": "p.Ile137Phe",
"transcript": "ENST00000508748.6",
"protein_id": "ENSP00000424865.2",
"transcript_support_level": 5,
"aa_start": 137,
"aa_end": null,
"aa_length": 570,
"cds_start": 409,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 579,
"cdna_end": null,
"cdna_length": 4518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "NM_001199919.2",
"protein_id": "NP_001186848.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 566,
"cds_start": 325,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 414,
"cdna_end": null,
"cdna_length": 2047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000509219.2",
"protein_id": "ENSP00000423389.2",
"transcript_support_level": 5,
"aa_start": 109,
"aa_end": null,
"aa_length": 566,
"cds_start": 325,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 417,
"cdna_end": null,
"cdna_length": 1952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000652468.1",
"protein_id": "ENSP00000499112.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 566,
"cds_start": 325,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 2060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000507554.2",
"protein_id": "ENSP00000425558.2",
"transcript_support_level": 4,
"aa_start": 109,
"aa_end": null,
"aa_length": 542,
"cds_start": 325,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 2735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000698526.1",
"protein_id": "ENSP00000513775.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 527,
"cds_start": 325,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 424,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
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"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000652222.2",
"protein_id": "ENSP00000499141.2",
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "NM_001367286.1",
"protein_id": "NP_001354215.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 501,
"cds_start": 325,
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"cdna_start": 414,
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"cdna_length": 5956,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
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"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000650642.1",
"protein_id": "ENSP00000498516.1",
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000698613.1",
"protein_id": "ENSP00000513839.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
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"cds_start": 325,
"cds_end": null,
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"cdna_start": 414,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.82A>T",
"hgvs_p": "p.Ile28Phe",
"transcript": "ENST00000651425.1",
"protein_id": "ENSP00000498986.1",
"transcript_support_level": null,
"aa_start": 28,
"aa_end": null,
"aa_length": 461,
"cds_start": 82,
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"cdna_start": 231,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.82A>T",
"hgvs_p": "p.Ile28Phe",
"transcript": "ENST00000698610.1",
"protein_id": "ENSP00000513837.1",
"transcript_support_level": null,
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},
{
"aa_ref": "I",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
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"exon_count": 12,
"intron_rank": null,
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"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.82A>T",
"hgvs_p": "p.Ile28Phe",
"transcript": "NM_001199918.2",
"protein_id": "NP_001186847.1",
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"aa_end": null,
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"feature": null
},
{
"aa_ref": "I",
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 2,
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"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.82A>T",
"hgvs_p": "p.Ile28Phe",
"transcript": "ENST00000698608.1",
"protein_id": "ENSP00000513835.1",
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"aa_start": 28,
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"cds_start": 82,
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"cdna_start": 188,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.82A>T",
"hgvs_p": "p.Ile28Phe",
"transcript": "ENST00000616566.5",
"protein_id": "ENSP00000477539.2",
"transcript_support_level": 2,
"aa_start": 28,
"aa_end": null,
"aa_length": 420,
"cds_start": 82,
"cds_end": null,
"cds_length": 1263,
"cdna_start": 177,
"cdna_end": null,
"cdna_length": 2325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "F",
"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": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe",
"transcript": "ENST00000698612.1",
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"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.257,
"revel_prediction": "Benign",
"alphamissense_score": 0.1234,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.707,
"phylop100way_prediction": "Uncertain_significance",
"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_Moderate,BP6,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000513973.6",
"gene_symbol": "PGM3",
"hgnc_id": 8907,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.325A>T",
"hgvs_p": "p.Ile109Phe"
}
],
"clinvar_disease": "Immunodeficiency 23,Inborn genetic diseases,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "Immunodeficiency 23|not specified|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}