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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: 2-127639407-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=127639407&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 127639407,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_017980.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.900C>T",
"hgvs_p": "p.Asp300Asp",
"transcript": "NM_001161403.3",
"protein_id": "NP_001154875.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 341,
"cds_start": 900,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000355119.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001161403.3"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.900C>T",
"hgvs_p": "p.Asp300Asp",
"transcript": "ENST00000355119.9",
"protein_id": "ENSP00000347240.4",
"transcript_support_level": 1,
"aa_start": 300,
"aa_end": null,
"aa_length": 341,
"cds_start": 900,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001161403.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355119.9"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.972C>T",
"hgvs_p": "p.Asp324Asp",
"transcript": "ENST00000324938.9",
"protein_id": "ENSP00000326888.5",
"transcript_support_level": 1,
"aa_start": 324,
"aa_end": null,
"aa_length": 365,
"cds_start": 972,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000324938.9"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.885C>T",
"hgvs_p": "p.Asp295Asp",
"transcript": "ENST00000409455.5",
"protein_id": "ENSP00000386383.1",
"transcript_support_level": 1,
"aa_start": 295,
"aa_end": null,
"aa_length": 336,
"cds_start": 885,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409455.5"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.885C>T",
"hgvs_p": "p.Asp295Asp",
"transcript": "ENST00000410011.5",
"protein_id": "ENSP00000387002.1",
"transcript_support_level": 1,
"aa_start": 295,
"aa_end": null,
"aa_length": 336,
"cds_start": 885,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000410011.5"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Asp148Asp",
"transcript": "ENST00000409754.5",
"protein_id": "ENSP00000386345.1",
"transcript_support_level": 1,
"aa_start": 148,
"aa_end": null,
"aa_length": 189,
"cds_start": 444,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409754.5"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1419C>T",
"hgvs_p": "p.Asp473Asp",
"transcript": "ENST00000855737.1",
"protein_id": "ENSP00000525796.1",
"transcript_support_level": null,
"aa_start": 473,
"aa_end": null,
"aa_length": 514,
"cds_start": 1419,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855737.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1308C>T",
"hgvs_p": "p.Asp436Asp",
"transcript": "ENST00000855740.1",
"protein_id": "ENSP00000525799.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 477,
"cds_start": 1308,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855740.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1296C>T",
"hgvs_p": "p.Asp432Asp",
"transcript": "ENST00000855742.1",
"protein_id": "ENSP00000525801.1",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 473,
"cds_start": 1296,
"cds_end": null,
"cds_length": 1422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855742.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1137C>T",
"hgvs_p": "p.Asp379Asp",
"transcript": "ENST00000957032.1",
"protein_id": "ENSP00000627091.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 420,
"cds_start": 1137,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957032.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.1074C>T",
"hgvs_p": "p.Asp358Asp",
"transcript": "ENST00000957031.1",
"protein_id": "ENSP00000627090.1",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 399,
"cds_start": 1074,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957031.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.978C>T",
"hgvs_p": "p.Asp326Asp",
"transcript": "ENST00000855738.1",
"protein_id": "ENSP00000525797.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 367,
"cds_start": 978,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855738.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.972C>T",
"hgvs_p": "p.Asp324Asp",
"transcript": "NM_017980.5",
"protein_id": "NP_060450.2",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 365,
"cds_start": 972,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017980.5"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.966C>T",
"hgvs_p": "p.Asp322Asp",
"transcript": "NM_001136037.4",
"protein_id": "NP_001129509.2",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 363,
"cds_start": 966,
"cds_end": null,
"cds_length": 1092,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001136037.4"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.966C>T",
"hgvs_p": "p.Asp322Asp",
"transcript": "ENST00000545738.6",
"protein_id": "ENSP00000443794.2",
"transcript_support_level": 5,
"aa_start": 322,
"aa_end": null,
"aa_length": 363,
"cds_start": 966,
"cds_end": null,
"cds_length": 1092,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000545738.6"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.960C>T",
"hgvs_p": "p.Asp320Asp",
"transcript": "ENST00000855739.1",
"protein_id": "ENSP00000525798.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 361,
"cds_start": 960,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855739.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.912C>T",
"hgvs_p": "p.Asp304Asp",
"transcript": "ENST00000855741.1",
"protein_id": "ENSP00000525800.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 345,
"cds_start": 912,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855741.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.885C>T",
"hgvs_p": "p.Asp295Asp",
"transcript": "NM_001161404.2",
"protein_id": "NP_001154876.1",
"transcript_support_level": null,
"aa_start": 295,
"aa_end": null,
"aa_length": 336,
"cds_start": 885,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001161404.2"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.885C>T",
"hgvs_p": "p.Asp295Asp",
"transcript": "ENST00000409808.6",
"protein_id": "ENSP00000386637.2",
"transcript_support_level": 5,
"aa_start": 295,
"aa_end": null,
"aa_length": 336,
"cds_start": 885,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409808.6"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.783C>T",
"hgvs_p": "p.Asp261Asp",
"transcript": "ENST00000855743.1",
"protein_id": "ENSP00000525802.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 302,
"cds_start": 783,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855743.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.777C>T",
"hgvs_p": "p.Asp259Asp",
"transcript": "ENST00000855744.1",
"protein_id": "ENSP00000525803.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 300,
"cds_start": 777,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855744.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.444C>T",
"hgvs_p": "p.Asp148Asp",
"transcript": "NM_001256542.2",
"protein_id": "NP_001243471.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 189,
"cds_start": 444,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001256542.2"
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"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6330000162124634,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.633,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.897,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP6_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_017980.5",
"gene_symbol": "LIMS2",
"hgnc_id": 16084,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.972C>T",
"hgvs_p": "p.Asp324Asp"
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2W",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2W",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}