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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: 22-41584045-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=41584045&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 41584045,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002676.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Glu130Lys",
"transcript": "NM_002676.3",
"protein_id": "NP_002667.2",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 262,
"cds_start": 388,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000216259.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002676.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Glu130Lys",
"transcript": "ENST00000216259.8",
"protein_id": "ENSP00000216259.7",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 262,
"cds_start": 388,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002676.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000216259.8"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "ENST00000949539.1",
"protein_id": "ENSP00000619598.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 340,
"cds_start": 622,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949539.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Glu173Lys",
"transcript": "ENST00000940470.1",
"protein_id": "ENSP00000610529.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 305,
"cds_start": 517,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940470.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.433G>A",
"hgvs_p": "p.Glu145Lys",
"transcript": "ENST00000949538.1",
"protein_id": "ENSP00000619597.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 277,
"cds_start": 433,
"cds_end": null,
"cds_length": 834,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949538.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Glu130Lys",
"transcript": "ENST00000949537.1",
"protein_id": "ENSP00000619596.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 271,
"cds_start": 388,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949537.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.409G>A",
"hgvs_p": "p.Glu137Lys",
"transcript": "ENST00000896620.1",
"protein_id": "ENSP00000566679.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 269,
"cds_start": 409,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896620.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Glu130Lys",
"transcript": "ENST00000949536.1",
"protein_id": "ENSP00000619595.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 262,
"cds_start": 388,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949536.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Glu130Lys",
"transcript": "ENST00000940468.1",
"protein_id": "ENSP00000610527.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 261,
"cds_start": 388,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940468.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Glu130Lys",
"transcript": "ENST00000940469.1",
"protein_id": "ENSP00000610528.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 260,
"cds_start": 388,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940469.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.382G>A",
"hgvs_p": "p.Glu128Lys",
"transcript": "ENST00000940471.1",
"protein_id": "ENSP00000610530.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 260,
"cds_start": 382,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940471.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.379G>A",
"hgvs_p": "p.Glu127Lys",
"transcript": "ENST00000896615.1",
"protein_id": "ENSP00000566674.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 259,
"cds_start": 379,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896615.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.355G>A",
"hgvs_p": "p.Glu119Lys",
"transcript": "ENST00000896617.1",
"protein_id": "ENSP00000566676.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 251,
"cds_start": 355,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896617.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Glu130Lys",
"transcript": "ENST00000896616.1",
"protein_id": "ENSP00000566675.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 240,
"cds_start": 388,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896616.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.296G>A",
"hgvs_p": "p.Arg99Gln",
"transcript": "ENST00000896618.1",
"protein_id": "ENSP00000566677.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 206,
"cds_start": 296,
"cds_end": null,
"cds_length": 621,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896618.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.178G>A",
"hgvs_p": "p.Glu60Lys",
"transcript": "ENST00000896619.1",
"protein_id": "ENSP00000566678.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 192,
"cds_start": 178,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896619.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Glu173Lys",
"transcript": "XM_011530229.3",
"protein_id": "XP_011528531.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 305,
"cds_start": 517,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530229.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.403G>A",
"hgvs_p": "p.Glu135Lys",
"transcript": "XM_011530230.3",
"protein_id": "XP_011528532.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 267,
"cds_start": 403,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530230.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.178G>A",
"hgvs_p": "p.Glu60Lys",
"transcript": "XM_011530231.4",
"protein_id": "XP_011528533.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 192,
"cds_start": 178,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530231.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.97G>A",
"hgvs_p": "p.Glu33Lys",
"transcript": "XM_005261638.5",
"protein_id": "XP_005261695.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 165,
"cds_start": 97,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005261638.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.97G>A",
"hgvs_p": "p.Glu33Lys",
"transcript": "XM_011530232.2",
"protein_id": "XP_011528534.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 165,
"cds_start": 97,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530232.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM1",
"gene_hgnc_id": 9114,
"hgvs_c": "c.43G>A",
"hgvs_p": "p.Glu15Lys",
"transcript": "XM_047441411.1",
"protein_id": "XP_047297367.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 147,
"cds_start": 43,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441411.1"
},
{
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],
"gene_symbol": "PMM1",
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"frequency_reference_population": 6.8439897e-7,
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"gnomad_exomes_af": 6.84399e-7,
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"computational_score_selected": 0.9793965816497803,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.979,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9917,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.79,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.11,
"spliceai_max_prediction": "Benign",
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"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
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"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_002676.3",
"gene_symbol": "PMM1",
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"effects": [
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],
"inheritance_mode": "AR",
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],
"clinvar_disease": " absent or hypoplastic corpus callosum, and dysmorphic facies,Global developmental delay",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}